Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine dr...

Full description

Saved in:
Bibliographic Details
Published inNature communications Vol. 13; no. 1; p. 2389
Main Authors Gao, Shaoming, Paez-Espino, David, Li, Jintian, Ai, Hongxia, Liang, Jieliang, Luo, Zhenhao, Zheng, Jin, Chen, Hao, Shu, Wensheng, Huang, Linan
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 02.05.2022
Nature Publishing Group
Nature Portfolio
Subjects
49/22
49/23
631/158/852
631/158/855
631/326/2565/2142
Acid mine drainage
Acids
Biodiversity
Biogeography
Biotic factors
Environmental conditions
Extreme environments
Extreme values
Humanities and Social Sciences
Mathematical analysis
Metagenome - genetics
Metagenomics
Mine drainage
Mining
multidisciplinary
Phosphorus
Science
Science & Technology - Other Topics
Science (multidisciplinary)
Sediments
Taxonomy
Viruses
Viruses - genetics
China
Online AccessGet full text

Cover

Abstract Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments. The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
AbstractList Abstract Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.
Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments. The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
Abstract Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.
Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.
The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage sediments sampled across Southern China, showing the predominant effects of prokaryotic communities and the influence of environmental variables on viral taxonomy and function.
ArticleNumber 2389
Author Liang, Jieliang
Shu, Wensheng
Huang, Linan
Ai, Hongxia
Luo, Zhenhao
Zheng, Jin
Li, Jintian
Gao, Shaoming
Paez-Espino, David
Chen, Hao
Author_xml – sequence: 1
  givenname: Shaoming
  orcidid: 0000-0001-7219-6485
  surname: Gao
  fullname: Gao, Shaoming
  organization: School of Life Sciences, Sun Yat-sen University
– sequence: 2
  givenname: David
  surname: Paez-Espino
  fullname: Paez-Espino, David
  organization: DOE Joint Genome Institute, Lawrence Berkeley National Laboratory
– sequence: 3
  givenname: Jintian
  surname: Li
  fullname: Li, Jintian
  organization: School of Life Sciences, South China Normal University
– sequence: 4
  givenname: Hongxia
  surname: Ai
  fullname: Ai, Hongxia
  organization: School of Life Sciences, Sun Yat-sen University
– sequence: 5
  givenname: Jieliang
  surname: Liang
  fullname: Liang, Jieliang
  organization: School of Life Sciences, South China Normal University
– sequence: 6
  givenname: Zhenhao
  surname: Luo
  fullname: Luo, Zhenhao
  organization: School of Life Sciences, Sun Yat-sen University
– sequence: 7
  givenname: Jin
  surname: Zheng
  fullname: Zheng, Jin
  organization: School of Life Sciences, South China Normal University
– sequence: 8
  givenname: Hao
  surname: Chen
  fullname: Chen, Hao
  organization: School of Environment and Energy, South China University of Technology
– sequence: 9
  givenname: Wensheng
  orcidid: 0000-0002-8743-1705
  surname: Shu
  fullname: Shu, Wensheng
  organization: School of Life Sciences, South China Normal University
– sequence: 10
  givenname: Linan
  orcidid: 0000-0002-4881-7920
  surname: Huang
  fullname: Huang, Linan
  email: eseshln@mail.sysu.edu.cn
  organization: School of Life Sciences, Sun Yat-sen University
BackLink https://www.ncbi.nlm.nih.gov/pubmed/35501347$$D View this record in MEDLINE/PubMed
https://www.osti.gov/servlets/purl/2470877$$D View this record in Osti.gov
BookMark eNp9kktvFSEYhiemxtbaP-DCEN24GeU6DBsTc-KlSRNN1DVh4JtzOJmBCsxJ_PfSM7W2LmQDgYfn4_I-bU5CDNA0zwl-QzDr32ZOeCdbTGnLMOaqFY-aM4o5aYmk7OTe-LS5yHmPa2OK9Jw_aU6ZEJgwLs-a_VdTCqSQkQkOgY1T3HprJuSSP0DKKI7o4FOdsHGel-CLh4x8QMZ6h2YfoJLGB7MFlMH5GUKpLptizuhbXMquytFmV4lnzePRTBkubvvz5sfHD983n9urL58uN--vWis6WVphekaM6jsHWA31kCMee-kUOAydVeMwSDOMRhmMDReCU-C8jpnFygAVHTtvLlevi2avr5OfTfqlo_H6OBHTVptUvJ1AK2575wYiMAgue6U4Z3SAjghn3TDi6nq3uq6XYQZn6-3qWzyQPlwJfqe38aAV7ojsVBW8XAUxF6-z9QXszsYQwBZNucS9lBV6fVslxZ8L5KJnny1MkwkQl6xpJxSlfdf1FX31D7qPSwr1PW-onmPFBa8UXanjPyQY705MsL6Jj17jo2t89DE-WtRNL-7f9W7Ln7BUgK1ArkthC-lv7f9ofwPVRtKo
CitedBy_id crossref_primary_10_1128_aem_01973_22
crossref_primary_10_1016_j_bsheal_2024_02_006
crossref_primary_10_1111_1462_2920_16329
crossref_primary_10_1038_s41598_023_28488_1
crossref_primary_10_1016_j_envint_2023_108055
crossref_primary_10_1016_j_envres_2024_119070
crossref_primary_10_1016_j_jare_2024_06_022
crossref_primary_10_1038_s41522_024_00522_8
crossref_primary_10_1016_j_jhazmat_2023_132088
crossref_primary_10_1016_j_envpol_2023_122667
crossref_primary_10_3389_fmicb_2023_1328158
crossref_primary_10_3390_biology12111411
crossref_primary_10_3390_fermentation10010010
crossref_primary_10_1016_j_chemosphere_2023_138412
crossref_primary_10_1017_S1473550423000058
crossref_primary_10_1016_j_syapm_2024_126519
crossref_primary_10_1002_ece3_11501
crossref_primary_10_1007_s10482_023_01912_2
crossref_primary_10_1016_j_watres_2024_121404
crossref_primary_10_1038_s41467_024_47214_7
crossref_primary_10_1016_j_watres_2023_120611
crossref_primary_10_1016_j_microb_2024_100042
crossref_primary_10_1021_acs_est_3c04398
crossref_primary_10_1016_j_soilbio_2024_109313
crossref_primary_10_1007_s11356_023_25408_8
crossref_primary_10_1038_s44221_024_00249_y
crossref_primary_10_2166_wst_2022_422
crossref_primary_10_3389_fmicb_2023_1125709
Cites_doi 10.1038/nprot.2017.063
10.1371/journal.pcbi.1002195
10.1073/pnas.1101595108
10.1126/science.1256688
10.1089/cmb.2012.0021
10.1038/s41559-020-01364-1
10.4319/lo.2001.46.7.1734
10.18637/jss.v048.i02
10.1093/femsre/fuv048
10.1186/1471-2105-11-119
10.1038/nature06810
10.3389/fmars.2016.00082
10.1186/s40168-019-0675-9
10.1038/s41586-018-0338-1
10.1038/s41396-020-0632-4
10.1016/j.cub.2011.11.055
10.1038/ismej.2014.245
10.1038/nature19094
10.1038/s41467-021-24803-4
10.1038/s41564-018-0190-y
10.1073/pnas.1319778111
10.1038/nbt.4306
10.1126/science.1157358
10.7717/peerj.997
10.1038/ismej.2015.201
10.1126/science.1153475
10.1038/s41587-019-0100-8
10.1038/nmeth.3103
10.1038/s41587-020-00774-7
10.1126/science.aam9974
10.1038/s41396-019-0580-z
10.1186/s12866-019-1445-3
10.1038/ismej.2012.147
10.1038/s41396-021-00897-y
10.1126/science.aaf4381
10.1093/bioinformatics/btv638
10.1093/molbev/msaa015
10.2136/sssaj1951.036159950015000C0032x
10.1126/science.1261498
10.1093/femsec/fiac002
10.1038/s41564-019-0426-5
10.1038/ismej.2009.31
10.1093/nar/gky1085
10.7554/eLife.08490
10.1128/mSystems.00385-21
10.7717/peerj.985
10.1128/AEM.05531-11
10.1038/s41564-018-0312-6
10.1080/01490450802402703
10.1093/nar/gkz239
10.1038/ismej.2012.139
10.1093/nar/gky995
10.1186/s40168-017-0301-7
10.7717/peerj.7359
10.1038/s41564-017-0012-7
10.1097/00010694-194501000-00006
10.1038/nrmicro3404
10.1038/s41564-018-0171-1
10.1007/s11783-014-0679-4
10.1186/s40168-020-00848-3
10.3389/fmicb.2017.01975
10.1126/science.1071698
10.1038/s41579-021-00602-y
10.1080/01490451.2013.770978
10.1371/journal.pgen.1002441
10.1016/j.cell.2019.03.040
10.1093/nar/gkv1070
10.1093/bioinformatics/bts565
10.1111/1758-2229.12504
10.1038/s42003-021-01810-1
10.1038/nature19366
10.1093/bioinformatics/btp348
10.1126/science.276.5313.734
10.1039/an9780300391
10.1038/nature14486
10.1073/pnas.0601301103
10.1111/j.1462-2920.2012.02879.x
10.1007/s12080-021-00508-8
10.1186/1471-2105-5-113
10.1073/pnas.1415442111
10.1016/j.mib.2010.01.014
10.1016/j.tim.2016.03.004
10.1093/gigascience/giab056
10.1101/gr.186072.114
10.1038/s41579-021-00648-y
10.1093/bioinformatics/btz848
10.1101/2020.09.08.284018
10.1111/j.1462-2920.2007.01444.x
10.1038/s41396-021-00947-5
ContentType Journal Article
Copyright The Author(s) 2022
2022. The Author(s).
The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
Copyright_xml – notice: The Author(s) 2022
– notice: 2022. The Author(s).
– notice: The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
CorporateAuthor Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
CorporateAuthor_xml – name: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
DBID C6C
CGR
CUY
CVF
ECM
EIF
NPM
AAYXX
CITATION
3V.
7QL
7QP
7QR
7SN
7SS
7ST
7T5
7T7
7TM
7TO
7X7
7XB
88E
8AO
8FD
8FE
8FG
8FH
8FI
8FJ
8FK
ABUWG
AFKRA
ARAPS
AZQEC
BBNVY
BENPR
BGLVJ
BHPHI
C1K
CCPQU
DWQXO
FR3
FYUFA
GHDGH
GNUQQ
H94
HCIFZ
K9.
LK8
M0S
M1P
M7P
P5Z
P62
P64
PIMPY
PQEST
PQQKQ
PQUKI
PRINS
RC3
SOI
7X8
OIOZB
OTOTI
5PM
DOA
DOI 10.1038/s41467-022-30049-5
DatabaseName Springer_OA刊
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
CrossRef
ProQuest Central (Corporate)
Bacteriology Abstracts (Microbiology B)
Calcium & Calcified Tissue Abstracts
Chemoreception Abstracts
Ecology Abstracts
Entomology Abstracts (Full archive)
Environment Abstracts
Immunology Abstracts
Industrial and Applied Microbiology Abstracts (Microbiology A)
Nucleic Acids Abstracts
Oncogenes and Growth Factors Abstracts
ProQuest Health & Medical Collection
ProQuest Central (purchase pre-March 2016)
Medical Database (Alumni Edition)
ProQuest Pharma Collection
Technology Research Database
ProQuest SciTech Collection
ProQuest Technology Collection
ProQuest Natural Science Collection
Hospital Premium Collection
Hospital Premium Collection (Alumni Edition)
ProQuest Central (Alumni) (purchase pre-March 2016)
ProQuest Central (Alumni)
ProQuest Central
Advanced Technologies & Aerospace Collection
ProQuest Central Essentials
Biological Science Collection
ProQuest Central
Technology Collection
ProQuest Natural Science Collection
Environmental Sciences and Pollution Management
ProQuest One Community College
ProQuest Central
Engineering Research Database
Health Research Premium Collection
Health Research Premium Collection (Alumni)
ProQuest Central Student
AIDS and Cancer Research Abstracts
SciTech Premium Collection (Proquest) (PQ_SDU_P3)
ProQuest Health & Medical Complete (Alumni)
Biological Sciences
Health & Medical Collection (Alumni Edition)
PML(ProQuest Medical Library)
Biological Science Database
Advanced Technologies & Aerospace Database
ProQuest Advanced Technologies & Aerospace Collection
Biotechnology and BioEngineering Abstracts
Publicly Available Content Database
ProQuest One Academic Eastern Edition (DO NOT USE)
ProQuest One Academic
ProQuest One Academic UKI Edition
ProQuest Central China
Genetics Abstracts
Environment Abstracts
MEDLINE - Academic
OSTI.GOV - Hybrid
OSTI.GOV
PubMed Central (Full Participant titles)
DOAJ Directory of Open Access Journals
DatabaseTitle MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
CrossRef
Publicly Available Content Database
ProQuest Central Student
Oncogenes and Growth Factors Abstracts
ProQuest Advanced Technologies & Aerospace Collection
ProQuest Central Essentials
Nucleic Acids Abstracts
SciTech Premium Collection
ProQuest Central China
Environmental Sciences and Pollution Management
Health Research Premium Collection
Natural Science Collection
Biological Science Collection
Chemoreception Abstracts
Industrial and Applied Microbiology Abstracts (Microbiology A)
ProQuest Medical Library (Alumni)
Advanced Technologies & Aerospace Collection
ProQuest Biological Science Collection
ProQuest One Academic Eastern Edition
ProQuest Hospital Collection
ProQuest Technology Collection
Health Research Premium Collection (Alumni)
Biological Science Database
Ecology Abstracts
ProQuest Hospital Collection (Alumni)
Biotechnology and BioEngineering Abstracts
Entomology Abstracts
ProQuest Health & Medical Complete
ProQuest One Academic UKI Edition
Engineering Research Database
ProQuest One Academic
Calcium & Calcified Tissue Abstracts
Technology Collection
Technology Research Database
ProQuest Health & Medical Complete (Alumni)
ProQuest Central (Alumni Edition)
ProQuest One Community College
ProQuest Natural Science Collection
ProQuest Pharma Collection
ProQuest Central
Genetics Abstracts
Health and Medicine Complete (Alumni Edition)
ProQuest Central Korea
Bacteriology Abstracts (Microbiology B)
AIDS and Cancer Research Abstracts
ProQuest SciTech Collection
Advanced Technologies & Aerospace Database
ProQuest Medical Library
Immunology Abstracts
Environment Abstracts
ProQuest Central (Alumni)
MEDLINE - Academic
DatabaseTitleList CrossRef



MEDLINE

Publicly Available Content Database
Database_xml – sequence: 1
  dbid: C6C
  name: Springer_OA刊
  url: http://www.springeropen.com/
  sourceTypes: Publisher
– sequence: 2
  dbid: DOA
  name: DOAJ Directory of Open Access Journals
  url: https://www.doaj.org/
  sourceTypes: Open Website
– sequence: 3
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 4
  dbid: EIF
  name: MEDLINE
  url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search
  sourceTypes: Index Database
– sequence: 5
  dbid: 8FG
  name: ProQuest Technology Collection
  url: https://search.proquest.com/technologycollection1
  sourceTypes: Aggregation Database
DeliveryMethod fulltext_linktorsrc
Discipline Biology
EISSN 2041-1723
EndPage 2389
ExternalDocumentID oai_doaj_org_article_94c8ddb150e5478994432be615dcdbf0
2470877
10_1038_s41467_022_30049_5
35501347
Genre Research Support, Non-U.S. Gov't
Journal Article
GeographicLocations China
GeographicLocations_xml – name: China
GrantInformation_xml – fundername: National Natural Science Foundation of China (National Science Foundation of China)
  grantid: 41830318; 31870111; 31570500
  funderid: https://doi.org/10.13039/501100001809
– fundername: Natural Science Foundation of Guangdong Province (2021A1515012468)
– fundername: ;
  grantid: 41830318; 31870111; 31570500
– fundername: ;
GroupedDBID ---
0R~
39C
3V.
53G
5VS
70F
7X7
88E
8AO
8FE
8FG
8FH
8FI
8FJ
AAHBH
AAJSJ
ABUWG
ACGFO
ACGFS
ACIWK
ACMJI
ACPRK
ACSMW
ADBBV
ADFRT
ADRAZ
AENEX
AFKRA
AFRAH
AHMBA
AJTQC
ALIPV
ALMA_UNASSIGNED_HOLDINGS
AMTXH
AOIJS
ARAPS
ASPBG
AVWKF
AZFZN
BBNVY
BCNDV
BENPR
BGLVJ
BHPHI
BPHCQ
BVXVI
C6C
CCPQU
DIK
EBLON
EBS
EE.
EMOBN
F5P
FEDTE
FYUFA
GROUPED_DOAJ
HCIFZ
HMCUK
HVGLF
HYE
HZ~
KQ8
LK8
M1P
M48
M7P
M~E
NAO
O9-
OK1
P2P
P62
PIMPY
PQQKQ
PROAC
PSQYO
RNS
RNT
RNTTT
RPM
SNYQT
SV3
TSG
UKHRP
CGR
CUY
CVF
ECM
EIF
NPM
AAYXX
CITATION
7QL
7QP
7QR
7SN
7SS
7ST
7T5
7T7
7TM
7TO
7XB
8FD
8FK
AZQEC
C1K
DWQXO
FR3
GNUQQ
H94
K9.
P64
PQEST
PQUKI
PRINS
RC3
SOI
7X8
OIOZB
OTOTI
5PM
ID FETCH-LOGICAL-c567t-5a831a986de09b347f0f87d9ed0e6c9fbb7abfa9a00a45542e44a003c09ae2563
IEDL.DBID RPM
ISSN 2041-1723
IngestDate Tue Oct 22 15:12:06 EDT 2024
Tue Sep 17 20:30:50 EDT 2024
Mon Oct 28 03:00:21 EDT 2024
Sat Oct 05 05:13:16 EDT 2024
Thu Oct 10 18:05:22 EDT 2024
Fri Aug 23 02:30:30 EDT 2024
Sat Sep 28 08:19:25 EDT 2024
Fri Oct 11 20:51:31 EDT 2024
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 1
Language English
License 2022. The Author(s).
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c567t-5a831a986de09b347f0f87d9ed0e6c9fbb7abfa9a00a45542e44a003c09ae2563
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
USDOE
AC02-05CH11231
ORCID 0000-0001-7219-6485
0000-0002-8743-1705
0000-0002-4881-7920
0000000248817920
0000000287431705
0000000172196485
OpenAccessLink https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9061769/
PMID 35501347
PQID 2658409454
PQPubID 546298
PageCount 1
ParticipantIDs doaj_primary_oai_doaj_org_article_94c8ddb150e5478994432be615dcdbf0
pubmedcentral_primary_oai_pubmedcentral_nih_gov_9061769
osti_scitechconnect_2470877
proquest_miscellaneous_2659228668
proquest_journals_2658409454
crossref_primary_10_1038_s41467_022_30049_5
pubmed_primary_35501347
springer_journals_10_1038_s41467_022_30049_5
PublicationCentury 2000
PublicationDate 2022-05-02
PublicationDateYYYYMMDD 2022-05-02
PublicationDate_xml – month: 05
  year: 2022
  text: 2022-05-02
  day: 02
PublicationDecade 2020
PublicationPlace London
PublicationPlace_xml – name: London
– name: England
– name: United States
PublicationTitle Nature communications
PublicationTitleAbbrev Nat Commun
PublicationTitleAlternate Nat Commun
PublicationYear 2022
Publisher Nature Publishing Group UK
Nature Publishing Group
Nature Portfolio
Publisher_xml – name: Nature Publishing Group UK
– name: Nature Publishing Group
– name: Nature Portfolio
References Kang (CR73) 2019; 7
Holmfeldt (CR22) 2021; 4
Capella-Gutiérrez, Silla-Martínez, Gabaldón (CR86) 2009; 25
Sullivan, Weitz, Wilhelm (CR10) 2017; 9
Adriaenssens (CR18) 2017; 5
Emerson (CR19) 2018; 3
Huerta-Cepas (CR30) 2019; 47
Martiny, Coleman, Chisholm (CR57) 2006; 103
Bray, Kurtz (CR61) 1945; 59
Chaumeil, Mussig, Hugenholtz, Parks (CR79) 2019; 36
Brum (CR13) 2015; 348
Kazakov, Vassieva, Gelfand, Osterman, Overbeek (CR60) 2003; 3
Wu, Simmons, Singer (CR74) 2016; 32
Zeng, Chisholm (CR59) 2012; 22
Fang (CR64) 2015; 9
Sun (CR39) 2013; 15
Narr, Nawaz, Wick, Harms, Chatzinotas (CR36) 2017; 8
Hyatt (CR66) 2010; 11
Kyle, Pedersen, Ferris (CR47) 2008; 25
Nayfach (CR27) 2021; 39
Sieber (CR77) 2018; 3
Harrell, Dupont (CR91) 2019; 4
CR3
Sant, Woods, Barr, McDonald (CR53) 2021; 5
Brown (CR75) 2015; 523
Green, Bohannan, Whitaker (CR6) 2008; 320
Hwang, Rahlff, Schulze-Makuch, Schloter, Probst (CR17) 2021; 6
Miraldo (CR44) 2016; 353
Kuang (CR52) 2013; 7
Gregory (CR14) 2019; 177
CR89
Wu (CR50) 2019; 4
Bankevich (CR65) 2012; 19
Parks (CR78) 2017; 2
Roux (CR71) 2016; 537
Kanehisa, Sato, Kawashima, Furumichi, Tanabe (CR68) 2016; 44
Alneberg (CR76) 2014; 11
Hewson, O’Neil, Fuhrman, Dennison (CR49) 2001; 46
El-Gebali (CR67) 2019; 47
Chesmin, Yien (CR63) 1951; 15
Betts, Gray, Zelek, MacLean, King (CR54) 2018; 360
Hsieh, Wanner (CR34) 2010; 13
Rho, Wu, Tang, Doak, Ye (CR83) 2012; 8
Torsvik, Øvreås, Thingstad (CR1) 2002; 296
Kuang (CR2) 2016; 10
Violle, Reich, Pacala, Enquist, Kattge (CR5) 2004; 111
Tetu (CR58) 2009; 3
Roux, Hallam, Woyke, Sullivan (CR70) 2015; 4
Flores, Meyer, Valverde, Farr, Weitz (CR94) 2011; 108
Paez-Espino, Pavlopoulos, Ivanova, Kyrpides (CR25) 2017; 12
Pace (CR4) 1997; 276
Stasi, Neves, Spira (CR35) 2019; 19
Tedersoo (CR43) 2014; 346
Hao (CR24) 2022; 98
Bin Jang (CR28) 2019; 37
Liang (CR33) 2020; 14
CR15
Roux, Enault, Hurwitz, Sullivan (CR26) 2015; 3
Howard-Varona (CR8) 2020; 14
Tyson, Banfield (CR38) 2008; 10
Goldsmith, Parsons, Beyene, Salamon, Breitbart (CR55) 2015; 3
CR92
CR90
Hill (CR62) 1978; 103
Rahlff (CR23) 2021; 12
Daly (CR7) 2019; 4
Edgar (CR85) 2004; 5
Huang, Kuang, Shu (CR16) 2016; 24
Jin (CR41) 2019; 7
Hurwitz, Westveld, Brum, Sullivan (CR40) 2014; 111
Bates (CR51) 2013; 7
CR29
Dinsdale (CR42) 2008; 452
Parks, Imelfort, Skennerton, Hugenholtz, Tyson (CR80) 2015; 25
Woodcroft (CR81) 2018; 560
Brum, Sullivan (CR11) 2015; 13
Gao (CR21) 2020; 8
Rosseel (CR93) 2012; 48
Roux (CR12) 2019; 37
Andersson, Banfield (CR20) 2008; 320
Wu (CR31) 2021; 10
Chen (CR32) 2015; 9
Eddy (CR69) 2011; 7
Edwards, McNair, Faust, Raes, Dutilh (CR82) 2016; 40
Chevallereau, Pons, van Houte, Westra (CR9) 2022; 20
Minh (CR87) 2020; 37
Paez-Espino (CR84) 2016; 536
Bonnain, Breitbart, Buck (CR45) 2016; 3
Kyle, Ferris (CR48) 2013; 30
Goldsmith (CR56) 2011; 77
Fu, Niu, Zhu, Wu, Li (CR72) 2012; 28
Santos-Medellin (CR37) 2021; 15
Letunic, Bork (CR88) 2019; 47
Muratore, Weitz (CR46) 2021; 14
AC Gregory (30049_CR14) 2019; 177
EM Adriaenssens (30049_CR18) 2017; 5
R Stasi (30049_CR35) 2019; 19
LX Chen (30049_CR32) 2015; 9
EA Dinsdale (30049_CR42) 2008; 452
RC Edgar (30049_CR85) 2004; 5
J Rahlff (30049_CR23) 2021; 12
A Narr (30049_CR36) 2017; 8
AC Martiny (30049_CR57) 2006; 103
30049_CR3
30049_CR29
JL Liang (30049_CR33) 2020; 14
YJ Hsieh (30049_CR34) 2010; 13
C Violle (30049_CR5) 2004; 111
JL Kuang (30049_CR52) 2013; 7
CO Flores (30049_CR94) 2011; 108
SG Tetu (30049_CR58) 2009; 3
M Kanehisa (30049_CR68) 2016; 44
S Wu (30049_CR31) 2021; 10
CL Sun (30049_CR39) 2013; 15
NR Pace (30049_CR4) 1997; 276
ST Bates (30049_CR51) 2013; 7
Q Zeng (30049_CR59) 2012; 22
AF Andersson (30049_CR20) 2008; 320
M Jin (30049_CR41) 2019; 7
DD Kang (30049_CR73) 2019; 7
PA Chaumeil (30049_CR79) 2019; 36
I Letunic (30049_CR88) 2019; 47
S Roux (30049_CR26) 2015; 3
AG Hill (30049_CR62) 1978; 103
RA Daly (30049_CR7) 2019; 4
S Roux (30049_CR12) 2019; 37
BL Hurwitz (30049_CR40) 2014; 111
L Tedersoo (30049_CR43) 2014; 346
A Chevallereau (30049_CR9) 2022; 20
S Nayfach (30049_CR27) 2021; 39
JE Kyle (30049_CR47) 2008; 25
YW Wu (30049_CR74) 2016; 32
I Hewson (30049_CR49) 2001; 46
DH Parks (30049_CR78) 2017; 2
BJ Woodcroft (30049_CR81) 2018; 560
A Bankevich (30049_CR65) 2012; 19
Y Fang (30049_CR64) 2015; 9
RA Edwards (30049_CR82) 2016; 40
CT Brown (30049_CR75) 2015; 523
C Bonnain (30049_CR45) 2016; 3
S Capella-Gutiérrez (30049_CR86) 2009; 25
DB Goldsmith (30049_CR56) 2011; 77
L Fu (30049_CR72) 2012; 28
DG Sant (30049_CR53) 2021; 5
CMK Sieber (30049_CR77) 2018; 3
S El-Gebali (30049_CR67) 2019; 47
30049_CR89
JL Green (30049_CR6) 2008; 320
D Paez-Espino (30049_CR25) 2017; 12
D Paez-Espino (30049_CR84) 2016; 536
A Betts (30049_CR54) 2018; 360
Y Hwang (30049_CR17) 2021; 6
D Muratore (30049_CR46) 2021; 14
J Huerta-Cepas (30049_CR30) 2019; 47
RH Bray (30049_CR61) 1945; 59
YQ Hao (30049_CR24) 2022; 98
H Bin Jang (30049_CR28) 2019; 37
DB Goldsmith (30049_CR55) 2015; 3
D Hyatt (30049_CR66) 2010; 11
JB Emerson (30049_CR19) 2018; 3
GW Tyson (30049_CR38) 2008; 10
M Rho (30049_CR83) 2012; 8
Y Rosseel (30049_CR93) 2012; 48
AE Kazakov (30049_CR60) 2003; 3
C Howard-Varona (30049_CR8) 2020; 14
SR Eddy (30049_CR69) 2011; 7
DH Parks (30049_CR80) 2015; 25
J Kuang (30049_CR2) 2016; 10
MB Sullivan (30049_CR10) 2017; 9
L Chesmin (30049_CR63) 1951; 15
FE Harrell Jr (30049_CR91) 2019; 4
30049_CR15
SM Gao (30049_CR21) 2020; 8
LN Huang (30049_CR16) 2016; 24
V Torsvik (30049_CR1) 2002; 296
C Santos-Medellin (30049_CR37) 2021; 15
K Holmfeldt (30049_CR22) 2021; 4
L Wu (30049_CR50) 2019; 4
S Roux (30049_CR71) 2016; 537
S Roux (30049_CR70) 2015; 4
BQ Minh (30049_CR87) 2020; 37
J Alneberg (30049_CR76) 2014; 11
JR Brum (30049_CR13) 2015; 348
JR Brum (30049_CR11) 2015; 13
30049_CR90
A Miraldo (30049_CR44) 2016; 353
JE Kyle (30049_CR48) 2013; 30
30049_CR92
References_xml – volume: 12
  start-page: 1673
  year: 2017
  end-page: 1682
  ident: CR25
  article-title: Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
  publication-title: Nat. Protoc.
  doi: 10.1038/nprot.2017.063
  contributor:
    fullname: Kyrpides
– volume: 7
  start-page: e1002195
  year: 2011
  ident: CR69
  article-title: Accelerated profile HMM searches
  publication-title: PLOS Comput. Biol.
  doi: 10.1371/journal.pcbi.1002195
  contributor:
    fullname: Eddy
– volume: 108
  start-page: E288
  year: 2011
  end-page: E297
  ident: CR94
  article-title: Statistical structure of host-phage interactions
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1101595108
  contributor:
    fullname: Weitz
– volume: 346
  start-page: 1256688
  year: 2014
  ident: CR43
  article-title: Fungal biogeography. Global diversity and geography of soil fungi
  publication-title: Science
  doi: 10.1126/science.1256688
  contributor:
    fullname: Tedersoo
– volume: 19
  start-page: 455
  year: 2012
  end-page: 477
  ident: CR65
  article-title: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing
  publication-title: J. Comput. Biol.
  doi: 10.1089/cmb.2012.0021
  contributor:
    fullname: Bankevich
– volume: 5
  start-page: 350
  year: 2021
  end-page: 359
  ident: CR53
  article-title: Host diversity slows bacteriophage adaptation by selecting generalists over specialists
  publication-title: Nat. Ecol. Evol.
  doi: 10.1038/s41559-020-01364-1
  contributor:
    fullname: McDonald
– volume: 46
  start-page: 1734
  year: 2001
  end-page: 1746
  ident: CR49
  article-title: Virus-like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries
  publication-title: Limnol. Oceanogr.
  doi: 10.4319/lo.2001.46.7.1734
  contributor:
    fullname: Dennison
– volume: 48
  start-page: 1
  year: 2012
  end-page: 36
  ident: CR93
  article-title: Lavaan: An R package for structural equation modeling and more. Version 0.5-12 (BETA)
  publication-title: J. Stat. Soft
  doi: 10.18637/jss.v048.i02
  contributor:
    fullname: Rosseel
– volume: 40
  start-page: 258
  year: 2016
  end-page: 272
  ident: CR82
  article-title: Computational approaches to predict bacteriophage-host relationships
  publication-title: FEMS Microbiol. Rev.
  doi: 10.1093/femsre/fuv048
  contributor:
    fullname: Dutilh
– volume: 11
  year: 2010
  ident: CR66
  article-title: Prodigal: prokaryotic gene recognition and translation initiation site identification
  publication-title: BMC Bioinforma.
  doi: 10.1186/1471-2105-11-119
  contributor:
    fullname: Hyatt
– volume: 452
  start-page: 629
  year: 2008
  end-page: 632
  ident: CR42
  article-title: Functional metagenomic profiling of nine biomes
  publication-title: Nature
  doi: 10.1038/nature06810
  contributor:
    fullname: Dinsdale
– volume: 3
  start-page: 82
  year: 2016
  ident: CR45
  article-title: The Ferrojan horse hypothesis: iron-virus interactions in the ocean
  publication-title: Front. Mar. Sci.
  doi: 10.3389/fmars.2016.00082
  contributor:
    fullname: Buck
– ident: CR29
– volume: 7
  year: 2019
  ident: CR41
  article-title: Diversities and potential biogeochemical impacts of mangrove soil viruses
  publication-title: Microbiome
  doi: 10.1186/s40168-019-0675-9
  contributor:
    fullname: Jin
– volume: 560
  start-page: 49
  year: 2018
  end-page: 54
  ident: CR81
  article-title: Genome-centric view of carbon processing in thawing permafrost
  publication-title: Nature
  doi: 10.1038/s41586-018-0338-1
  contributor:
    fullname: Woodcroft
– volume: 14
  start-page: 1600
  year: 2020
  end-page: 1613
  ident: CR33
  article-title: Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining
  publication-title: ISME J.
  doi: 10.1038/s41396-020-0632-4
  contributor:
    fullname: Liang
– volume: 22
  start-page: 124
  year: 2012
  end-page: 128
  ident: CR59
  article-title: Marine viruses exploit their host’s two-component regulatory system in response to resource limitation
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2011.11.055
  contributor:
    fullname: Chisholm
– volume: 9
  start-page: 1579
  year: 2015
  end-page: 1592
  ident: CR32
  article-title: Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage
  publication-title: ISME J.
  doi: 10.1038/ismej.2014.245
  contributor:
    fullname: Chen
– volume: 536
  start-page: 425
  year: 2016
  end-page: 430
  ident: CR84
  article-title: Uncovering Earth’s virome
  publication-title: Nature
  doi: 10.1038/nature19094
  contributor:
    fullname: Paez-Espino
– volume: 12
  year: 2021
  ident: CR23
  article-title: Lytic archaeal viruses infect abundant primary producers in Earth’s crust
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-24803-4
  contributor:
    fullname: Rahlff
– volume: 3
  start-page: 870
  year: 2018
  end-page: 880
  ident: CR19
  article-title: Host-linked soil viral ecology along a permafrost thaw gradient
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-018-0190-y
  contributor:
    fullname: Emerson
– volume: 111
  start-page: 10714
  year: 2014
  end-page: 10719
  ident: CR40
  article-title: Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1319778111
  contributor:
    fullname: Sullivan
– volume: 36
  start-page: 1925
  year: 2019
  end-page: 1927
  ident: CR79
  article-title: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
  publication-title: Bioinformatics
  contributor:
    fullname: Parks
– ident: CR92
– volume: 37
  start-page: 29
  year: 2019
  end-page: 37
  ident: CR12
  article-title: Minimum information about an uncultivated virus genome (MIUViG)
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.4306
  contributor:
    fullname: Roux
– ident: CR15
– volume: 320
  start-page: 1047
  year: 2008
  end-page: 1050
  ident: CR20
  article-title: Virus population dynamics and acquired virus resistance in natural microbial communities
  publication-title: Science
  doi: 10.1126/science.1157358
  contributor:
    fullname: Banfield
– volume: 3
  start-page: e997
  year: 2015
  ident: CR55
  article-title: Deep sequencing of the viral gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral genes in the Sargasso Sea
  publication-title: Peer. J.
  doi: 10.7717/peerj.997
  contributor:
    fullname: Breitbart
– volume: 10
  start-page: 1527
  year: 2016
  end-page: 1539
  ident: CR2
  article-title: Predicting taxonomic and functional structure of microbial communities in acid mine drainage
  publication-title: ISME J.
  doi: 10.1038/ismej.2015.201
  contributor:
    fullname: Kuang
– volume: 320
  start-page: 1039
  year: 2008
  end-page: 1043
  ident: CR6
  article-title: Microbial biogeography: from taxonomy to traits
  publication-title: Science
  doi: 10.1126/science.1153475
  contributor:
    fullname: Whitaker
– volume: 37
  start-page: 632
  year: 2019
  end-page: 639
  ident: CR28
  article-title: Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-019-0100-8
  contributor:
    fullname: Bin Jang
– volume: 11
  start-page: 1144
  year: 2014
  end-page: 1146
  ident: CR76
  article-title: Binning metagenomic contigs by coverage and composition
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.3103
  contributor:
    fullname: Alneberg
– volume: 39
  start-page: 578
  year: 2021
  end-page: 585
  ident: CR27
  article-title: CheckV: assessing the quality of metagenome-assembled viral genomes
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-020-00774-7
  contributor:
    fullname: Nayfach
– volume: 4
  start-page: 2
  year: 2019
  end-page: 0
  ident: CR91
  article-title: The hmisc package
  publication-title: R. package version
  contributor:
    fullname: Dupont
– volume: 360
  start-page: 907
  year: 2018
  end-page: 911
  ident: CR54
  article-title: High parasite diversity accelerates host adaptation and diversification
  publication-title: Science
  doi: 10.1126/science.aam9974
  contributor:
    fullname: King
– volume: 14
  start-page: 881
  year: 2020
  end-page: 895
  ident: CR8
  article-title: Phage-specific metabolic reprogramming of virocells
  publication-title: ISME J.
  doi: 10.1038/s41396-019-0580-z
  contributor:
    fullname: Howard-Varona
– volume: 19
  start-page: 79
  year: 2019
  ident: CR35
  article-title: Phosphate uptake by the phosphonate transport system PhnCDE
  publication-title: BMC Microbiol
  doi: 10.1186/s12866-019-1445-3
  contributor:
    fullname: Spira
– volume: 7
  start-page: 652
  year: 2013
  end-page: 659
  ident: CR51
  article-title: Global biogeography of highly diverse protistan communities in soil
  publication-title: ISME J.
  doi: 10.1038/ismej.2012.147
  contributor:
    fullname: Bates
– volume: 15
  start-page: 1956
  year: 2021
  end-page: 1970
  ident: CR37
  article-title: Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities
  publication-title: ISME J.
  doi: 10.1038/s41396-021-00897-y
  contributor:
    fullname: Santos-Medellin
– volume: 353
  start-page: 1532
  year: 2016
  end-page: 1535
  ident: CR44
  article-title: An Anthropocene map of genetic diversity
  publication-title: Science
  doi: 10.1126/science.aaf4381
  contributor:
    fullname: Miraldo
– volume: 32
  start-page: 605
  year: 2016
  end-page: 607
  ident: CR74
  article-title: MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv638
  contributor:
    fullname: Singer
– volume: 37
  start-page: 1530
  year: 2020
  end-page: 1534
  ident: CR87
  article-title: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msaa015
  contributor:
    fullname: Minh
– volume: 15
  start-page: 149
  year: 1951
  end-page: 151
  ident: CR63
  article-title: Turbidimetric determination of available sulphate
  publication-title: Soil Sci. Soc. Am. Proc.
  doi: 10.2136/sssaj1951.036159950015000C0032x
  contributor:
    fullname: Yien
– volume: 348
  start-page: 1261498
  year: 2015
  ident: CR13
  article-title: Patterns and ecological drivers of ocean viral communities
  publication-title: Science
  doi: 10.1126/science.1261498
  contributor:
    fullname: Brum
– volume: 98
  start-page: fiac002
  year: 2022
  ident: CR24
  article-title: Microbial biogeography of acid mine drainage sediments at a regional scale across Southern China
  publication-title: FEMS Microbiol. Ecol.
  doi: 10.1093/femsec/fiac002
  contributor:
    fullname: Hao
– volume: 4
  start-page: 1183
  year: 2019
  end-page: 1195
  ident: CR50
  article-title: Global diversity and biogeography of bacterial communities in wastewater treatment plants
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-019-0426-5
  contributor:
    fullname: Wu
– volume: 3
  start-page: 835
  year: 2009
  end-page: 849
  ident: CR58
  article-title: Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp. WH8102
  publication-title: ISME J.
  doi: 10.1038/ismej.2009.31
  contributor:
    fullname: Tetu
– volume: 47
  start-page: D309
  year: 2019
  end-page: D314
  ident: CR30
  article-title: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gky1085
  contributor:
    fullname: Huerta-Cepas
– volume: 4
  start-page: e08490
  year: 2015
  ident: CR70
  article-title: Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
  publication-title: Elife
  doi: 10.7554/eLife.08490
  contributor:
    fullname: Sullivan
– ident: CR89
– volume: 6
  start-page: e00385
  year: 2021
  end-page: 21
  ident: CR17
  article-title: Diverse viruses carrying genes for microbial extremotolerance in the Atacama desert hyperarid soil
  publication-title: mSystems
  doi: 10.1128/mSystems.00385-21
  contributor:
    fullname: Probst
– volume: 3
  start-page: e985
  year: 2015
  ident: CR26
  article-title: VirSorter: mining viral signal from microbial genomic data
  publication-title: PeerJ
  doi: 10.7717/peerj.985
  contributor:
    fullname: Sullivan
– volume: 77
  start-page: 7730
  year: 2011
  end-page: 7739
  ident: CR56
  article-title: Development of as a novel signature gene for assessing marine phage diversity
  publication-title: Appl. Environ. Microbiol.
  doi: 10.1128/AEM.05531-11
  contributor:
    fullname: Goldsmith
– volume: 4
  start-page: 352
  year: 2019
  end-page: 361
  ident: CR7
  article-title: Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-018-0312-6
  contributor:
    fullname: Daly
– volume: 25
  start-page: 338
  year: 2008
  end-page: 345
  ident: CR47
  article-title: Virus mineralization at low pH in the Rio Tinto
  publication-title: Spain Geomicrobiol. J.
  doi: 10.1080/01490450802402703
  contributor:
    fullname: Ferris
– volume: 47
  start-page: W256
  year: 2019
  end-page: W259
  ident: CR88
  article-title: Interactive Tree Of Life (iTOL) v4: recent updates and new developments
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkz239
  contributor:
    fullname: Bork
– volume: 7
  start-page: 1038
  year: 2013
  end-page: 1050
  ident: CR52
  article-title: Contemporary environmental variation determines microbial diversity patterns in acid mine drainage
  publication-title: ISME J.
  doi: 10.1038/ismej.2012.139
  contributor:
    fullname: Kuang
– volume: 47
  start-page: D427
  year: 2019
  end-page: D432
  ident: CR67
  article-title: The Pfam protein families database in 2019
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gky995
  contributor:
    fullname: El-Gebali
– volume: 5
  year: 2017
  ident: CR18
  article-title: Environmental drivers of viral community composition in Antarctic soils identified by viromics
  publication-title: Microbiome
  doi: 10.1186/s40168-017-0301-7
  contributor:
    fullname: Adriaenssens
– volume: 7
  start-page: e7359
  year: 2019
  ident: CR73
  article-title: MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
  publication-title: PeerJ
  doi: 10.7717/peerj.7359
  contributor:
    fullname: Kang
– volume: 2
  start-page: 1533
  year: 2017
  end-page: 1542
  ident: CR78
  article-title: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-017-0012-7
  contributor:
    fullname: Parks
– volume: 59
  start-page: 39
  year: 1945
  end-page: 46
  ident: CR61
  article-title: Determination of total, organic, and available forms of phosphorus in soils
  publication-title: Soil Sci.
  doi: 10.1097/00010694-194501000-00006
  contributor:
    fullname: Kurtz
– volume: 13
  start-page: 147
  year: 2015
  end-page: 159
  ident: CR11
  article-title: Rising to the challenge: accelerated pace of discovery transforms marine virology
  publication-title: Nat. Rev. Microbiol.
  doi: 10.1038/nrmicro3404
  contributor:
    fullname: Sullivan
– volume: 3
  start-page: 836
  year: 2018
  end-page: 843
  ident: CR77
  article-title: Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-018-0171-1
  contributor:
    fullname: Sieber
– volume: 9
  start-page: 444
  year: 2015
  end-page: 452
  ident: CR64
  article-title: Modified pretreatment method for total microbial DNA extraction from contaminated river sediment
  publication-title: Front. Environ. Sci. Eng.
  doi: 10.1007/s11783-014-0679-4
  contributor:
    fullname: Fang
– volume: 8
  year: 2020
  ident: CR21
  article-title: Depth-related variability in viral communities in highly stratified sulfidic mine tailings
  publication-title: Microbiome
  doi: 10.1186/s40168-020-00848-3
  contributor:
    fullname: Gao
– volume: 8
  start-page: 1975
  year: 2017
  ident: CR36
  article-title: Soil viral communities vary temporally and along a land use transect as revealed by virus-like particle counting and a modified community fingerprinting approach (fRAPD)
  publication-title: Front. Microbiol.
  doi: 10.3389/fmicb.2017.01975
  contributor:
    fullname: Chatzinotas
– volume: 296
  start-page: 1064
  year: 2002
  end-page: 1066
  ident: CR1
  article-title: Prokaryotic diversity-magnitude, dynamics, and controlling factors
  publication-title: Science
  doi: 10.1126/science.1071698
  contributor:
    fullname: Thingstad
– volume: 20
  start-page: 49
  year: 2022
  end-page: 62
  ident: CR9
  article-title: Interactions between bacterial and phage communities in natural environments
  publication-title: Nat. Rev. Microbiol.
  doi: 10.1038/s41579-021-00602-y
  contributor:
    fullname: Westra
– ident: CR90
– volume: 30
  start-page: 769
  year: 2013
  end-page: 778
  ident: CR48
  article-title: Geochemistry of virus–prokaryote interactions in freshwater and acid mine drainage environments, Ontario, Canada
  publication-title: Geomicrobiol. J.
  doi: 10.1080/01490451.2013.770978
  contributor:
    fullname: Ferris
– volume: 8
  start-page: e1002441
  year: 2012
  ident: CR83
  article-title: Diverse CRISPRs evolving in human microbiomes
  publication-title: PLoS Genet.
  doi: 10.1371/journal.pgen.1002441
  contributor:
    fullname: Ye
– ident: CR3
– volume: 177
  start-page: 1109
  year: 2019
  end-page: 1123
  ident: CR14
  article-title: Marine DNA viral macro- and microdiversity from pole to pole
  publication-title: Cell
  doi: 10.1016/j.cell.2019.03.040
  contributor:
    fullname: Gregory
– volume: 44
  start-page: D457
  year: 2016
  end-page: D462
  ident: CR68
  article-title: KEGG as a reference resource for gene and protein annotation
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkv1070
  contributor:
    fullname: Tanabe
– volume: 28
  start-page: 3150
  year: 2012
  end-page: 3152
  ident: CR72
  article-title: CD-HIT: accelerated for clustering the next- generation sequencing data
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts565
  contributor:
    fullname: Li
– volume: 9
  start-page: 33
  year: 2017
  end-page: 35
  ident: CR10
  article-title: Viral ecology comes of age
  publication-title: Environ. Microbiol. Rep.
  doi: 10.1111/1758-2229.12504
  contributor:
    fullname: Wilhelm
– volume: 4
  start-page: 307
  year: 2021
  ident: CR22
  article-title: The Fennoscandian Shield deep terrestrial virosphere suggests slow motion ‘boom and burst’ cycles
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-021-01810-1
  contributor:
    fullname: Holmfeldt
– volume: 10
  start-page: 200
  year: 2008
  end-page: 207
  ident: CR38
  article-title: Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
  publication-title: Environ. Microbiol.
  contributor:
    fullname: Banfield
– volume: 537
  start-page: 689
  year: 2016
  end-page: 693
  ident: CR71
  article-title: Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
  publication-title: Nature
  doi: 10.1038/nature19366
  contributor:
    fullname: Roux
– volume: 25
  start-page: 1972
  year: 2009
  end-page: 1973
  ident: CR86
  article-title: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp348
  contributor:
    fullname: Gabaldón
– volume: 276
  start-page: 734
  year: 1997
  end-page: 740
  ident: CR4
  article-title: A molecular view of microbial diversity and the biosphere
  publication-title: Science
  doi: 10.1126/science.276.5313.734
  contributor:
    fullname: Pace
– volume: 103
  start-page: 391
  year: 1978
  end-page: 396
  ident: CR62
  article-title: Standardized general method for the determination of iron with 1,10-phenanthroline
  publication-title: Analyst
  doi: 10.1039/an9780300391
  contributor:
    fullname: Hill
– volume: 523
  start-page: 208
  year: 2015
  end-page: 201
  ident: CR75
  article-title: Unusual biology across a group comprising more than 15% of domain Bacteria
  publication-title: Nature
  doi: 10.1038/nature14486
  contributor:
    fullname: Brown
– volume: 103
  start-page: 12552
  year: 2006
  end-page: 12557
  ident: CR57
  article-title: Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.0601301103
  contributor:
    fullname: Chisholm
– volume: 15
  start-page: 463
  year: 2013
  end-page: 470
  ident: CR39
  article-title: Phage mutations in response to CRISPR diversification in a bacterial population
  publication-title: Environ. Microbiol.
  doi: 10.1111/j.1462-2920.2012.02879.x
  contributor:
    fullname: Sun
– volume: 14
  start-page: 467
  year: 2021
  end-page: 487
  ident: CR46
  article-title: Infect while the iron is scarce: nutrient-explicit phage-bacteria games
  publication-title: Theor. Ecol.
  doi: 10.1007/s12080-021-00508-8
  contributor:
    fullname: Weitz
– volume: 5
  year: 2004
  ident: CR85
  article-title: MUSCLE: a multiple sequence alignment method with reduced time and space complexity
  publication-title: BMC Bioinforma.
  doi: 10.1186/1471-2105-5-113
  contributor:
    fullname: Edgar
– volume: 111
  start-page: 13690
  year: 2004
  end-page: 13696
  ident: CR5
  article-title: The emergence and promise of functional biogeography
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1415442111
  contributor:
    fullname: Kattge
– volume: 13
  start-page: 198
  year: 2010
  end-page: 203
  ident: CR34
  article-title: Global regulation by the seven-component Pi signaling system
  publication-title: Curr. Opin. Microbiol.
  doi: 10.1016/j.mib.2010.01.014
  contributor:
    fullname: Wanner
– volume: 24
  start-page: 581
  year: 2016
  end-page: 593
  ident: CR16
  article-title: Microbial ecology and evolution in the acid mine drainage model system
  publication-title: Trends Microbiol
  doi: 10.1016/j.tim.2016.03.004
  contributor:
    fullname: Shu
– volume: 10
  year: 2021
  ident: CR31
  article-title: DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach
  publication-title: Gigascience
  doi: 10.1093/gigascience/giab056
  contributor:
    fullname: Wu
– volume: 25
  start-page: 1043
  year: 2015
  end-page: 1055
  ident: CR80
  article-title: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  publication-title: Genome Res
  doi: 10.1101/gr.186072.114
  contributor:
    fullname: Tyson
– volume: 3
  start-page: 3
  year: 2003
  end-page: 15
  ident: CR60
  article-title: Bioinformatics classification and functional analysis of PhoH homologs
  publication-title: Silico Biol.
  contributor:
    fullname: Overbeek
– volume: 3
  start-page: 835
  year: 2009
  ident: 30049_CR58
  publication-title: ISME J.
  doi: 10.1038/ismej.2009.31
  contributor:
    fullname: SG Tetu
– volume: 320
  start-page: 1039
  year: 2008
  ident: 30049_CR6
  publication-title: Science
  doi: 10.1126/science.1153475
  contributor:
    fullname: JL Green
– volume: 28
  start-page: 3150
  year: 2012
  ident: 30049_CR72
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts565
  contributor:
    fullname: L Fu
– volume: 2
  start-page: 1533
  year: 2017
  ident: 30049_CR78
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-017-0012-7
  contributor:
    fullname: DH Parks
– ident: 30049_CR89
– volume: 177
  start-page: 1109
  year: 2019
  ident: 30049_CR14
  publication-title: Cell
  doi: 10.1016/j.cell.2019.03.040
  contributor:
    fullname: AC Gregory
– volume: 4
  start-page: e08490
  year: 2015
  ident: 30049_CR70
  publication-title: Elife
  doi: 10.7554/eLife.08490
  contributor:
    fullname: S Roux
– volume: 15
  start-page: 463
  year: 2013
  ident: 30049_CR39
  publication-title: Environ. Microbiol.
  doi: 10.1111/j.1462-2920.2012.02879.x
  contributor:
    fullname: CL Sun
– ident: 30049_CR15
  doi: 10.1038/s41579-021-00648-y
– volume: 3
  start-page: e997
  year: 2015
  ident: 30049_CR55
  publication-title: Peer. J.
  doi: 10.7717/peerj.997
  contributor:
    fullname: DB Goldsmith
– volume: 19
  start-page: 79
  year: 2019
  ident: 30049_CR35
  publication-title: BMC Microbiol
  doi: 10.1186/s12866-019-1445-3
  contributor:
    fullname: R Stasi
– volume: 77
  start-page: 7730
  year: 2011
  ident: 30049_CR56
  publication-title: Appl. Environ. Microbiol.
  doi: 10.1128/AEM.05531-11
  contributor:
    fullname: DB Goldsmith
– volume: 25
  start-page: 1043
  year: 2015
  ident: 30049_CR80
  publication-title: Genome Res
  doi: 10.1101/gr.186072.114
  contributor:
    fullname: DH Parks
– volume: 47
  start-page: W256
  year: 2019
  ident: 30049_CR88
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkz239
  contributor:
    fullname: I Letunic
– volume: 12
  year: 2021
  ident: 30049_CR23
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-24803-4
  contributor:
    fullname: J Rahlff
– volume: 452
  start-page: 629
  year: 2008
  ident: 30049_CR42
  publication-title: Nature
  doi: 10.1038/nature06810
  contributor:
    fullname: EA Dinsdale
– volume: 25
  start-page: 1972
  year: 2009
  ident: 30049_CR86
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp348
  contributor:
    fullname: S Capella-Gutiérrez
– volume: 9
  start-page: 1579
  year: 2015
  ident: 30049_CR32
  publication-title: ISME J.
  doi: 10.1038/ismej.2014.245
  contributor:
    fullname: LX Chen
– volume: 7
  start-page: 652
  year: 2013
  ident: 30049_CR51
  publication-title: ISME J.
  doi: 10.1038/ismej.2012.147
  contributor:
    fullname: ST Bates
– volume: 108
  start-page: E288
  year: 2011
  ident: 30049_CR94
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1101595108
  contributor:
    fullname: CO Flores
– volume: 37
  start-page: 29
  year: 2019
  ident: 30049_CR12
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.4306
  contributor:
    fullname: S Roux
– volume: 560
  start-page: 49
  year: 2018
  ident: 30049_CR81
  publication-title: Nature
  doi: 10.1038/s41586-018-0338-1
  contributor:
    fullname: BJ Woodcroft
– volume: 13
  start-page: 198
  year: 2010
  ident: 30049_CR34
  publication-title: Curr. Opin. Microbiol.
  doi: 10.1016/j.mib.2010.01.014
  contributor:
    fullname: YJ Hsieh
– volume: 5
  year: 2004
  ident: 30049_CR85
  publication-title: BMC Bioinforma.
  doi: 10.1186/1471-2105-5-113
  contributor:
    fullname: RC Edgar
– volume: 348
  start-page: 1261498
  year: 2015
  ident: 30049_CR13
  publication-title: Science
  doi: 10.1126/science.1261498
  contributor:
    fullname: JR Brum
– volume: 47
  start-page: D309
  year: 2019
  ident: 30049_CR30
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gky1085
  contributor:
    fullname: J Huerta-Cepas
– volume: 59
  start-page: 39
  year: 1945
  ident: 30049_CR61
  publication-title: Soil Sci.
  doi: 10.1097/00010694-194501000-00006
  contributor:
    fullname: RH Bray
– volume: 3
  start-page: 82
  year: 2016
  ident: 30049_CR45
  publication-title: Front. Mar. Sci.
  doi: 10.3389/fmars.2016.00082
  contributor:
    fullname: C Bonnain
– volume: 20
  start-page: 49
  year: 2022
  ident: 30049_CR9
  publication-title: Nat. Rev. Microbiol.
  doi: 10.1038/s41579-021-00602-y
  contributor:
    fullname: A Chevallereau
– volume: 39
  start-page: 578
  year: 2021
  ident: 30049_CR27
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-020-00774-7
  contributor:
    fullname: S Nayfach
– volume: 4
  start-page: 2
  year: 2019
  ident: 30049_CR91
  publication-title: R. package version
  contributor:
    fullname: FE Harrell Jr
– volume: 24
  start-page: 581
  year: 2016
  ident: 30049_CR16
  publication-title: Trends Microbiol
  doi: 10.1016/j.tim.2016.03.004
  contributor:
    fullname: LN Huang
– volume: 36
  start-page: 1925
  year: 2019
  ident: 30049_CR79
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btz848
  contributor:
    fullname: PA Chaumeil
– ident: 30049_CR90
– volume: 320
  start-page: 1047
  year: 2008
  ident: 30049_CR20
  publication-title: Science
  doi: 10.1126/science.1157358
  contributor:
    fullname: AF Andersson
– volume: 4
  start-page: 1183
  year: 2019
  ident: 30049_CR50
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-019-0426-5
  contributor:
    fullname: L Wu
– volume: 14
  start-page: 1600
  year: 2020
  ident: 30049_CR33
  publication-title: ISME J.
  doi: 10.1038/s41396-020-0632-4
  contributor:
    fullname: JL Liang
– volume: 537
  start-page: 689
  year: 2016
  ident: 30049_CR71
  publication-title: Nature
  doi: 10.1038/nature19366
  contributor:
    fullname: S Roux
– volume: 3
  start-page: 3
  year: 2003
  ident: 30049_CR60
  publication-title: Silico Biol.
  contributor:
    fullname: AE Kazakov
– volume: 111
  start-page: 13690
  year: 2004
  ident: 30049_CR5
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1415442111
  contributor:
    fullname: C Violle
– ident: 30049_CR29
  doi: 10.1101/2020.09.08.284018
– volume: 25
  start-page: 338
  year: 2008
  ident: 30049_CR47
  publication-title: Spain Geomicrobiol. J.
  doi: 10.1080/01490450802402703
  contributor:
    fullname: JE Kyle
– volume: 523
  start-page: 208
  year: 2015
  ident: 30049_CR75
  publication-title: Nature
  doi: 10.1038/nature14486
  contributor:
    fullname: CT Brown
– volume: 40
  start-page: 258
  year: 2016
  ident: 30049_CR82
  publication-title: FEMS Microbiol. Rev.
  doi: 10.1093/femsre/fuv048
  contributor:
    fullname: RA Edwards
– volume: 12
  start-page: 1673
  year: 2017
  ident: 30049_CR25
  publication-title: Nat. Protoc.
  doi: 10.1038/nprot.2017.063
  contributor:
    fullname: D Paez-Espino
– volume: 37
  start-page: 632
  year: 2019
  ident: 30049_CR28
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-019-0100-8
  contributor:
    fullname: H Bin Jang
– volume: 7
  start-page: 1038
  year: 2013
  ident: 30049_CR52
  publication-title: ISME J.
  doi: 10.1038/ismej.2012.139
  contributor:
    fullname: JL Kuang
– volume: 8
  start-page: e1002441
  year: 2012
  ident: 30049_CR83
  publication-title: PLoS Genet.
  doi: 10.1371/journal.pgen.1002441
  contributor:
    fullname: M Rho
– volume: 111
  start-page: 10714
  year: 2014
  ident: 30049_CR40
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1319778111
  contributor:
    fullname: BL Hurwitz
– volume: 7
  start-page: e7359
  year: 2019
  ident: 30049_CR73
  publication-title: PeerJ
  doi: 10.7717/peerj.7359
  contributor:
    fullname: DD Kang
– volume: 15
  start-page: 1956
  year: 2021
  ident: 30049_CR37
  publication-title: ISME J.
  doi: 10.1038/s41396-021-00897-y
  contributor:
    fullname: C Santos-Medellin
– volume: 346
  start-page: 1256688
  year: 2014
  ident: 30049_CR43
  publication-title: Science
  doi: 10.1126/science.1256688
  contributor:
    fullname: L Tedersoo
– volume: 9
  start-page: 444
  year: 2015
  ident: 30049_CR64
  publication-title: Front. Environ. Sci. Eng.
  doi: 10.1007/s11783-014-0679-4
  contributor:
    fullname: Y Fang
– volume: 10
  start-page: 1527
  year: 2016
  ident: 30049_CR2
  publication-title: ISME J.
  doi: 10.1038/ismej.2015.201
  contributor:
    fullname: J Kuang
– volume: 19
  start-page: 455
  year: 2012
  ident: 30049_CR65
  publication-title: J. Comput. Biol.
  doi: 10.1089/cmb.2012.0021
  contributor:
    fullname: A Bankevich
– volume: 6
  start-page: e00385
  year: 2021
  ident: 30049_CR17
  publication-title: mSystems
  doi: 10.1128/mSystems.00385-21
  contributor:
    fullname: Y Hwang
– volume: 15
  start-page: 149
  year: 1951
  ident: 30049_CR63
  publication-title: Soil Sci. Soc. Am. Proc.
  doi: 10.2136/sssaj1951.036159950015000C0032x
  contributor:
    fullname: L Chesmin
– volume: 14
  start-page: 467
  year: 2021
  ident: 30049_CR46
  publication-title: Theor. Ecol.
  doi: 10.1007/s12080-021-00508-8
  contributor:
    fullname: D Muratore
– volume: 14
  start-page: 881
  year: 2020
  ident: 30049_CR8
  publication-title: ISME J.
  doi: 10.1038/s41396-019-0580-z
  contributor:
    fullname: C Howard-Varona
– volume: 46
  start-page: 1734
  year: 2001
  ident: 30049_CR49
  publication-title: Limnol. Oceanogr.
  doi: 10.4319/lo.2001.46.7.1734
  contributor:
    fullname: I Hewson
– volume: 10
  start-page: 200
  year: 2008
  ident: 30049_CR38
  publication-title: Environ. Microbiol.
  doi: 10.1111/j.1462-2920.2007.01444.x
  contributor:
    fullname: GW Tyson
– volume: 4
  start-page: 352
  year: 2019
  ident: 30049_CR7
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-018-0312-6
  contributor:
    fullname: RA Daly
– volume: 3
  start-page: 870
  year: 2018
  ident: 30049_CR19
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-018-0190-y
  contributor:
    fullname: JB Emerson
– volume: 536
  start-page: 425
  year: 2016
  ident: 30049_CR84
  publication-title: Nature
  doi: 10.1038/nature19094
  contributor:
    fullname: D Paez-Espino
– volume: 47
  start-page: D427
  year: 2019
  ident: 30049_CR67
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gky995
  contributor:
    fullname: S El-Gebali
– volume: 11
  year: 2010
  ident: 30049_CR66
  publication-title: BMC Bioinforma.
  doi: 10.1186/1471-2105-11-119
  contributor:
    fullname: D Hyatt
– volume: 30
  start-page: 769
  year: 2013
  ident: 30049_CR48
  publication-title: Geomicrobiol. J.
  doi: 10.1080/01490451.2013.770978
  contributor:
    fullname: JE Kyle
– volume: 3
  start-page: 836
  year: 2018
  ident: 30049_CR77
  publication-title: Nat. Microbiol.
  doi: 10.1038/s41564-018-0171-1
  contributor:
    fullname: CMK Sieber
– volume: 276
  start-page: 734
  year: 1997
  ident: 30049_CR4
  publication-title: Science
  doi: 10.1126/science.276.5313.734
  contributor:
    fullname: NR Pace
– volume: 32
  start-page: 605
  year: 2016
  ident: 30049_CR74
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv638
  contributor:
    fullname: YW Wu
– ident: 30049_CR92
– volume: 353
  start-page: 1532
  year: 2016
  ident: 30049_CR44
  publication-title: Science
  doi: 10.1126/science.aaf4381
  contributor:
    fullname: A Miraldo
– volume: 103
  start-page: 391
  year: 1978
  ident: 30049_CR62
  publication-title: Analyst
  doi: 10.1039/an9780300391
  contributor:
    fullname: AG Hill
– volume: 7
  year: 2019
  ident: 30049_CR41
  publication-title: Microbiome
  doi: 10.1186/s40168-019-0675-9
  contributor:
    fullname: M Jin
– volume: 296
  start-page: 1064
  year: 2002
  ident: 30049_CR1
  publication-title: Science
  doi: 10.1126/science.1071698
  contributor:
    fullname: V Torsvik
– volume: 98
  start-page: fiac002
  year: 2022
  ident: 30049_CR24
  publication-title: FEMS Microbiol. Ecol.
  doi: 10.1093/femsec/fiac002
  contributor:
    fullname: YQ Hao
– volume: 7
  start-page: e1002195
  year: 2011
  ident: 30049_CR69
  publication-title: PLOS Comput. Biol.
  doi: 10.1371/journal.pcbi.1002195
  contributor:
    fullname: SR Eddy
– volume: 4
  start-page: 307
  year: 2021
  ident: 30049_CR22
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-021-01810-1
  contributor:
    fullname: K Holmfeldt
– volume: 8
  start-page: 1975
  year: 2017
  ident: 30049_CR36
  publication-title: Front. Microbiol.
  doi: 10.3389/fmicb.2017.01975
  contributor:
    fullname: A Narr
– volume: 44
  start-page: D457
  year: 2016
  ident: 30049_CR68
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkv1070
  contributor:
    fullname: M Kanehisa
– volume: 3
  start-page: e985
  year: 2015
  ident: 30049_CR26
  publication-title: PeerJ
  doi: 10.7717/peerj.985
  contributor:
    fullname: S Roux
– volume: 5
  year: 2017
  ident: 30049_CR18
  publication-title: Microbiome
  doi: 10.1186/s40168-017-0301-7
  contributor:
    fullname: EM Adriaenssens
– volume: 103
  start-page: 12552
  year: 2006
  ident: 30049_CR57
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.0601301103
  contributor:
    fullname: AC Martiny
– volume: 48
  start-page: 1
  year: 2012
  ident: 30049_CR93
  publication-title: J. Stat. Soft
  doi: 10.18637/jss.v048.i02
  contributor:
    fullname: Y Rosseel
– volume: 13
  start-page: 147
  year: 2015
  ident: 30049_CR11
  publication-title: Nat. Rev. Microbiol.
  doi: 10.1038/nrmicro3404
  contributor:
    fullname: JR Brum
– volume: 9
  start-page: 33
  year: 2017
  ident: 30049_CR10
  publication-title: Environ. Microbiol. Rep.
  doi: 10.1111/1758-2229.12504
  contributor:
    fullname: MB Sullivan
– volume: 11
  start-page: 1144
  year: 2014
  ident: 30049_CR76
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.3103
  contributor:
    fullname: J Alneberg
– volume: 37
  start-page: 1530
  year: 2020
  ident: 30049_CR87
  publication-title: Mol. Biol. Evol.
  doi: 10.1093/molbev/msaa015
  contributor:
    fullname: BQ Minh
– ident: 30049_CR3
  doi: 10.1038/s41396-021-00947-5
– volume: 8
  year: 2020
  ident: 30049_CR21
  publication-title: Microbiome
  doi: 10.1186/s40168-020-00848-3
  contributor:
    fullname: SM Gao
– volume: 22
  start-page: 124
  year: 2012
  ident: 30049_CR59
  publication-title: Curr. Biol.
  doi: 10.1016/j.cub.2011.11.055
  contributor:
    fullname: Q Zeng
– volume: 360
  start-page: 907
  year: 2018
  ident: 30049_CR54
  publication-title: Science
  doi: 10.1126/science.aam9974
  contributor:
    fullname: A Betts
– volume: 5
  start-page: 350
  year: 2021
  ident: 30049_CR53
  publication-title: Nat. Ecol. Evol.
  doi: 10.1038/s41559-020-01364-1
  contributor:
    fullname: DG Sant
– volume: 10
  year: 2021
  ident: 30049_CR31
  publication-title: Gigascience
  doi: 10.1093/gigascience/giab056
  contributor:
    fullname: S Wu
SSID ssj0000391844
Score 2.5948234
Snippet Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of...
Abstract Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our...
Abstract Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our...
The biogeography of viral communities in extreme environments remains understudied. Here, the authors use metagenomic sequencing on 90 acid mine drainage...
SourceID doaj
pubmedcentral
osti
proquest
crossref
pubmed
springer
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
Publisher
StartPage 2389
SubjectTerms 49/22
49/23
631/158/852
631/158/855
631/326/2565/2142
Acid mine drainage
Acids
Biodiversity
Biogeography
Biotic factors
Environmental conditions
Extreme environments
Extreme values
Humanities and Social Sciences
Mathematical analysis
Metagenome - genetics
Metagenomics
Mine drainage
Mining
multidisciplinary
Phosphorus
Science
Science & Technology - Other Topics
Science (multidisciplinary)
Sediments
Taxonomy
Viruses
Viruses - genetics
SummonAdditionalLinks – databaseName: DOAJ Directory of Open Access Journals
  dbid: DOA
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1LbxQxDLZQJSQuiPIcWlCQuMGoaZLJTI4FUVUcEAcq9Rbl4cAimEXd7YF_j52ZXbo8xIXTjjbRaBLb8WfF_gzwXAWCnYihDSmX1lDA3EaNXZtTNMXFZB3WBNl39uzcvL3oLq61-uKcsIkeeNq4I2fSkHMk3IJMPeWcMVpFJEecU45litaluxZM1TNYOwpdzFwlI_VwtDL1TKjJ6wyL227HE1XCfvpZkmH9CWz-njP5y8Vp9Uend-D2DCTFybSAfbiB4124ObWW_H4PPr-vxJnjSoQxC0ybM07ky5qJIZZFcH7vF5GmEhEmVhWLUYS0yOIrYU-ayZVVH1GsyMHVSjga5KWI2nePXi5q9-37cH765sPrs3buq9CmzvbrtguDPg5usBmli9r0RZahzw6zRJtcibEPsQQXpAyG4IZCY-hZJ-kCEkTSD2BvXI74CAS5wNTRW4s1xchSQgkESZTtjzMqibGBF5s99t8m-gxfr7314CeJeJKIrxLxXQOvWAzbmUx9Xf8ghfCzQvh_KUQDByxETwiCaXAT5wultVemZ-7DBg43svWzta68YhhGcW5nGni2HSY748uTMOLyqs5xSg3WDg08nFRh-52E2SSX5DbQ7yjJzkJ2R8bFp8rl7RhCWtfAy406_fysv2_U4_-xUQdwS7E5cPamOoS99eUVPiGEtY5PqzH9AHUJI5E
  priority: 102
  providerName: Directory of Open Access Journals
– databaseName: ProQuest Technology Collection
  dbid: 8FG
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Lb9QwEB5BERKXijehBRmJG0T1Ok5inxAglooD4kCl3iw_y1aQlM320H_PjJNstbxOWcVWNs7MeD7bM98AvBQWYWeMtrQ-pFLigrl0VazL4J1M2vlGxxwg-7k5PpGfTuvTacNtmMIq5zkxT9Sh97RHfiTIVeJapJZvLn6WVDWKTlenEho34dZCtC0tvtTy43aPhdjPlZRTrgyv1NEg88yQQ9gJHJf1jj_KtP146dG8_gY5_4yc_O34NHul5V3Yn-AkezvK_x7ciN19uD0WmLx6AOdfMn1mNzDbBRb9PNOxsM7xGKxPjKJ8vzM_JooQvSpbdcz6VWA_EIFiT8qvOotsQDeX8-GwkYbCcvU9fDjLNbgfwsnyw9f3x-VUXaH0ddNuytqqamG1akLk2lWyTTypNugYeGy8Ts611iWrLedWIugQUUr8XXmubUSgVD2Cva7v4hNg6Ah9jU9NjUySp2STRWAimnYRouDRFfBq_sbmYiTRMPnwu1JmlIhBiZgsEVMX8I7EsO1JBNj5Rr8-M5M9GS29CsEhnI3ESKa1xD90EfFZ8MElXsABCdEgjiAyXE9RQ35jhGyJAbGAw1m2ZrLZwVxrWAEvts1obXSEYrvYX-Y-WgjVNKqAx6MqbN8TkRunxNwC2h0l2RnIbku3-pYZvTUByUYX8HpWp-vX-veHevr_URzAHUGKTtGZ4hD2NuvL-AwR1MY9z2byC63FGvQ
  priority: 102
  providerName: ProQuest
– databaseName: Scholars Portal Journals: Open Access
  dbid: M48
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Lb9QwEB6VIiQuiPJqaEFG4gYB13Gc-IAQRVQVB8SBlXqz_CyLSlJ2txL998w4yaKFReKUKHYSxzMTfyPPfAPwXFiEnTHa0vqQSokOc-mqWJfBO5m080rHHCD7SZ3O5Mez-mwHpnJH4wQut7p2VE9qtrh49fPH9Vs0-DdDynj7eimzuee4dEK8ZX0DbgqJnjqF8o1wP_-ZK40OjRxzZ7bfurE-ZRp_PPRobtsg6N-RlH9sp-ZV6uQu3BnhJXs36MMe7MTuHtwaCk5e34dvnzOdZrdktgss-unPx8Iix2ewPjGK-r1gfkgcIbpVNu-Y9fPAviMixZ6Ub3Ue2RKXvZwfh430KSxX48OHs1yT-wHMTj58eX9ajtUWSl-rZlXWtq2OrG5ViFy7SjaJp7YJOgYeldfJuca6ZLXl3EoEISJKieeV59pGBE7VQ9jt-i7uA8OF0df41KRkkjwlmywCFaGaoxAFj66AF9Mcm8uBVMPkzfCqNYNEDErEZImYuoBjEsO6JxFi5wv94tyM9mW09G0IDuFtJIYyrSW-0EXEa8EHl3gBByREg7iCyHE9RRH5lRGyIUbEAg4n2ZpJBY0gcIbeby0LeLZuRuujLRXbxf4q99FCtEq1BTwaVGE9TkRynBJ1C2g2lGTjQzZbuvnXzPCtCVgqXcDLSZ1-D-vfE_X4P4Z5ALcFaTuFbIpD2F0truIThFUr9zTbyi8qpyAl
  priority: 102
  providerName: Scholars Portal
– databaseName: Springer_OA刊
  dbid: C6C
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwlV1Lb9QwEB5BERIXxJvQgozEDSJcx3HsI6yoKg6IA5V6s_wYwyLIou72wL9nxskuWigHToliJ7E9M5nP8cxngBcqEOxEDG1IubSaJsxt7LBvc4q6uJiMwxog-8Gcnun35_35TJPDuTB76_edfb3W1ZRrzDmj2ba_DjfIB1sO31qYxe5_CjOdW63nvJirb93zPZWinw4rMqWr4OXfUZJ_LJVWD3RyB27P0FG8mWR9F67heA9uTptJ_rwPXz9WqsxxLcKYBabtV03kixp7IVZFcETvN5GmpBCmUhXLUYS0zOI7oU2qyblUn1GsyaXV3Dcq5K6IutMePVzU_bYfwNnJu0-L03beSaFNvRk2bR9sdxycNRmli50eiix2yA6zRJNciXEIsQQXpAyaAIZCrem8S9IFJFDUPYSDcTXiYxDk9FJPTy1GFy1LCSUQCFFmOM6oJMYGXm7H2P-YCDN8XejurJ8k4kkivkrE9w28ZTHsajLZdb1AOuBn2_FOJ5tzJOiKzD7mnKYXRiQsllOORTZwyEL0hBmY-DZxhFDaeKUHZjts4GgrWz_b59orBl40s-11A893xWRZvFwSRlxd1jpOKWuMbeDRpAq7dhJKk5yE28CwpyR7HdkvGZdfKnu3Y9BoXAOvtur0u1n_Hqgn_1f9EG4pVnyOzFRHcLC5uMSnhJ428Vk1m1_PARPH
  priority: 102
  providerName: Springer Nature
Title Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China
URI https://link.springer.com/article/10.1038/s41467-022-30049-5
https://www.ncbi.nlm.nih.gov/pubmed/35501347
https://www.proquest.com/docview/2658409454
https://search.proquest.com/docview/2659228668
https://www.osti.gov/servlets/purl/2470877
https://pubmed.ncbi.nlm.nih.gov/PMC9061769
https://doaj.org/article/94c8ddb150e5478994432be615dcdbf0
Volume 13
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwED9tQ0i8IL4JG5WReIOsXuI48WNXrUyVNlXApL5Z_tyK1mRquwf-e85OUigfL7wkUWwlju_O93P8uzPA-0wh7HROpcpYnzKcMKc6d0VqjWZeaMOFiwTZS35-xabzYr4HRR8LE0n7Ri-O69vlcb24idzKu6UZ9jyx4exiLILf5WK4D_uooL9M0ePwmwuctbAuQIbm1XDN4nAQeesBEadhuxr0szSEUe74o5i2H08NmtffIOefzMnflk-jV5o8gccdnCSjttlPYc_Vz-Bhu8Hk9-fwbRbTZ9ZrompLnOlHOmJXkY9BGk8Cy_eWmDZQJKRXJYuaKLOwZIkIFGuG-KprR9bo5mI8HBaGTyFx9z18OIl7cL-Aq8nZ1_F52u2ukJqCl5u0UFV-okTFraNCY0946qvSCmep40Z4rUulvRKKUsUQdGSOMbzODRXKIVDKX8JB3dTuNRB0hKbAp3rOPKPeK68QmGS8PLEuo04n8KHvY3nXJtGQcfE7r2QrHInCkVE4skjgNIhhWzMkwI43mtW17NRACmYqazXCWRcykgnB8IXaIT6zxmpPEzgMQpSII0IyXBNYQ2YjM1aGDIgJHPWylZ3NrmUWwBjOdguWwLttMVpbWEJRtWvuYx2RZRXnVQKvWlXYtrPXqATKHSXZ-ZDdElTwmNG7U-gEPvbq9LNZ_-6oN__9okN4lAVzCMTN7AgONqt79xbB1UYP0KTmJR6ryacBPBiNpl-meD49u5x9xrtjPh7E3xZ4vGDVIJreD8SeK4E
link.rule.ids 230,315,730,783,787,867,888,2109,12068,12777,21400,24330,27936,27937,31731,31732,33385,33386,33756,33757,41132,42201,43322,43612,43817,51588,53804,53806,74073,74363,74630
linkProvider National Library of Medicine
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Lb9QwEB5BEaIXxLuhBYzEDaK6jvPwCQFiWaBUHFqpN8vPsgiSstke-PfMOMlWy-uUKLaSODPj-WLPfAPwTBiEnSGY3Dgfc4k_zLktQpl7Z2VU1lUqpADZo2p-Ij-clqfjgls_hlVOc2KaqH3naI18X5CrxH-RUr48_5FT1SjaXR1LaFyFa7JAX02Z4rN36zUWYj9vpBxzZXjR7PcyzQwphJ3AcV5u-KNE24-HDs3rb5Dzz8jJ37ZPk1ea3YKbI5xkrwb534Yrob0D14cCkz_vwtfPiT6z7ZlpPQtumumYX6Z4DNZFRlG-35gbEkWIXpUtWmbcwrPviECxJ-VXnQXWo5tL-XDYSENhqfoe3pylGtz34GT29vjNPB-rK-SurOpVXpqmODCqqXzgyhayjjw2tVfB81A5Fa2tjY1GGc6NRNAhgpR4XjiuTECgVNyHrbZrww4wdISuxLvGSkbJYzTRIDARVX3gg-DBZvB8-sb6fCDR0Gnzu2j0IBGNEtFJIrrM4DWJYd2TCLDThW55pkd70kq6xnuLcDYQI5lSEh9oA-Iz77yNPINdEqJGHEFkuI6ihtxKC1kTA2IGe5Ns9Wizvb7UsAyerpvR2mgLxbShu0h9lBBNVTUZPBhUYf2eiNw4JeZmUG8oycZANlvaxZfE6K0ISFYqgxeTOl2-1r8_1MP_j-IJ3JgffzrUh--PPu7CtiClp0hNsQdbq-VFeIRoamUfJ5P5BfmFHdY
linkToPdf http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwfV1Lb9QwEB5BEYgL4t3QAkbiBtG6iePEJ8RrVR6qeqDS3iw_yyKalM32wL9nxkm2Wl6nXa2tbJyZsT_H33wD8LwwCDtDMLlxPuYCN8y5LUOVe2dFVNZJFRJB9kgenoiPi2ox8p_6kVY5zYlpovado3fks4KWStyLVGIWR1rE8bv5q_MfOVWQopPWsZzGVbhW4y6FfL5e1Jv3LaSE3ggx5s3wspn1Is0Sic5OQDmvttamJOGPHx2G2t_g558syt-OUtMKNb8Nt0ZoyV4PvnAHroT2Llwfik3-vAffjpOUZtsz03oW3DTrMb9K3AzWRUaM3-_MDUkjJLXKli0zbunZGaJR7Em5VqeB9bjkpdw4bKShsFSJDy_OUj3u-3Ayf__l7WE-VlrIXSXrdV6ZpjwwqpE-cGVLUUcem9qr4HmQTkVra2OjUYZzIxCAFEEI_F46rkxA0FQ-gJ22a8MuMFwUXYVXjVJEwWM00SBIKWR94EPBg83gxfSM9fkgqKHTQXjZ6MEiGi2ik0V0lcEbMsOmJ4lhpx-61akeY0sr4RrvLULbQOpkSgn8QxsQq3nnbeQZ7JERNWIKEsZ1xCBya12ImtQQM9ifbKvH-O31pbdl8GzTjJFHxymmDd1F6qOKopGyyeDh4Aqb-0QUxylJN4N6y0m2BrLd0i6_JnVvRaBSqgxeTu50eVv_flCP_j-Kp3ADo0V__nD0aQ9uFuTzRNos9mFnvboIjxFYre2TFDG_AH-GIg4
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Patterns+and+ecological+drivers+of+viral+communities+in+acid+mine+drainage+sediments+across+Southern+China&rft.jtitle=Nature+communications&rft.au=Gao%2C+Shaoming&rft.au=Paez-Espino%2C+David&rft.au=Li%2C+Jintian&rft.au=Ai%2C+Hongxia&rft.date=2022-05-02&rft.eissn=2041-1723&rft.volume=13&rft.issue=1&rft.spage=2389&rft.epage=2389&rft_id=info:doi/10.1038%2Fs41467-022-30049-5&rft.externalDBID=NO_FULL_TEXT
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2041-1723&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2041-1723&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2041-1723&client=summon