Microbial community structure and functional potential along a hypersaline gradient

J.A. Kimbrel, N. Ballor, Y.-W. Wu, M.M. David, T.C. Hazen, B.A. Simmons, S.W. Singer, J.K. Jansson

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants. © 2018 Kimbrel, Ballor, Wu, David, Hazen, Simmons, Singer and Jansson.
Original languageEnglish
JournalFrontiers in Microbiology
Volume9
Issue numberJUL
DOIs
Publication statusPublished - 2018
Externally publishedYes

Fingerprint

Salinity
Enzymes
Carbohydrates
Metagenome
Metagenomics
San Francisco
Biofuels
Isoelectric Point
Firearms
Carbohydrate Metabolism
Oligosaccharides
Cellulose
Starch
Salts
Genome
Amino Acids
Water
DNA

Keywords

  • 16S rRNA
  • Biofuels
  • Halophiles
  • Metagenomes
  • Microbial communities
  • RNA 16S
  • starch
  • water
  • amino acid metabolism
  • Article
  • chemical analysis
  • DNA extraction
  • enzyme activity
  • gene sequence
  • hypersaline gradient
  • metagenome
  • methanogenesis
  • microbial community
  • microbiological parameters
  • nonhuman
  • open reading frame
  • salinity
  • sediment

Cite this

Kimbrel, J. A., Ballor, N., Wu, Y-W., David, M. M., Hazen, T. C., Simmons, B. A., ... Jansson, J. K. (2018). Microbial community structure and functional potential along a hypersaline gradient. Frontiers in Microbiology, 9(JUL). https://doi.org/10.3389/fmicb.2018.01492

Microbial community structure and functional potential along a hypersaline gradient. / Kimbrel, J.A.; Ballor, N.; Wu, Y.-W.; David, M.M.; Hazen, T.C.; Simmons, B.A.; Singer, S.W.; Jansson, J.K.

In: Frontiers in Microbiology, Vol. 9, No. JUL, 2018.

Research output: Contribution to journalArticle

Kimbrel, JA, Ballor, N, Wu, Y-W, David, MM, Hazen, TC, Simmons, BA, Singer, SW & Jansson, JK 2018, 'Microbial community structure and functional potential along a hypersaline gradient', Frontiers in Microbiology, vol. 9, no. JUL. https://doi.org/10.3389/fmicb.2018.01492
Kimbrel, J.A. ; Ballor, N. ; Wu, Y.-W. ; David, M.M. ; Hazen, T.C. ; Simmons, B.A. ; Singer, S.W. ; Jansson, J.K. / Microbial community structure and functional potential along a hypersaline gradient. In: Frontiers in Microbiology. 2018 ; Vol. 9, No. JUL.
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abstract = "Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2{\%}) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants. {\circledC} 2018 Kimbrel, Ballor, Wu, David, Hazen, Simmons, Singer and Jansson.",
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note = "Export Date: 2 October 2018 通訊地址: Jansson, J.K.; Microbial Communities Group, Deconstruction Division, Joint BioEnergy InstituteUnited States; 電子郵件: janet.jansson@pnnl.gov 化學物質/CAS: starch, 9005-25-8, 9005-84-9; water, 7732-18-5 參考文獻: Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K.L., Tyson, G.W., Nielsen, P.H., Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes (2013) Nat. Biotechnol, 31, pp. 533-538; Andrei, A.-S., Banciu, H.L., Oren, A., Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems (2012) FEMS Microbiol. Lett, 330, pp. 1-9; Athearn, N.D., Takekawa, J.Y., Bluso-Demers, J.D., Shinn, J.M., Brand, L.A., Robinson-Nilsen, C.W., Variability in habitat value of commercial salt production ponds: implications for waterbird management and tidal marsh restoration planning (2012) Hydrobiologia, 697, pp. 139-155; Barber{\'a}n, A., Bates, S.T., Casamayor, E.O., Fierer, N., Using network analysis to explore co-occurrence patterns in soil microbial communities (2012) ISME J, 6, pp. 343-351; Benlloch, S., L{\'o}pez-L{\'o}pez, A., Casamayor, E.O., {\O}vre{\aa}s, L., Goddard, V., Daae, F.L., Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern (2002) Environ. Microbiol, 4, pp. 349-360; Berlemont, R., Martiny, A.C., Phylogenetic distribution of potential cellulases in bacteria (2013) Appl. Environ. Microbiol, 79, pp. 1545-1554; Berlemont, R., Martiny, A.C., Genomic potential for polysaccharide deconstruction in bacteria (2015) Appl. Environ. 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TY - JOUR

T1 - Microbial community structure and functional potential along a hypersaline gradient

AU - Kimbrel, J.A.

AU - Ballor, N.

AU - Wu, Y.-W.

AU - David, M.M.

AU - Hazen, T.C.

AU - Simmons, B.A.

AU - Singer, S.W.

AU - Jansson, J.K.

N1 - Export Date: 2 October 2018 通訊地址: Jansson, J.K.; Microbial Communities Group, Deconstruction Division, Joint BioEnergy InstituteUnited States; 電子郵件: janet.jansson@pnnl.gov 化學物質/CAS: starch, 9005-25-8, 9005-84-9; water, 7732-18-5 參考文獻: Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K.L., Tyson, G.W., Nielsen, P.H., Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes (2013) Nat. Biotechnol, 31, pp. 533-538; Andrei, A.-S., Banciu, H.L., Oren, A., Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems (2012) FEMS Microbiol. Lett, 330, pp. 1-9; Athearn, N.D., Takekawa, J.Y., Bluso-Demers, J.D., Shinn, J.M., Brand, L.A., Robinson-Nilsen, C.W., Variability in habitat value of commercial salt production ponds: implications for waterbird management and tidal marsh restoration planning (2012) Hydrobiologia, 697, pp. 139-155; Barberán, A., Bates, S.T., Casamayor, E.O., Fierer, N., Using network analysis to explore co-occurrence patterns in soil microbial communities (2012) ISME J, 6, pp. 343-351; Benlloch, S., López-López, A., Casamayor, E.O., Øvreås, L., Goddard, V., Daae, F.L., Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern (2002) Environ. Microbiol, 4, pp. 349-360; Berlemont, R., Martiny, A.C., Phylogenetic distribution of potential cellulases in bacteria (2013) Appl. Environ. Microbiol, 79, pp. 1545-1554; Berlemont, R., Martiny, A.C., Genomic potential for polysaccharide deconstruction in bacteria (2015) Appl. Environ. 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PY - 2018

Y1 - 2018

N2 - Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants. © 2018 Kimbrel, Ballor, Wu, David, Hazen, Simmons, Singer and Jansson.

AB - Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants. © 2018 Kimbrel, Ballor, Wu, David, Hazen, Simmons, Singer and Jansson.

KW - 16S rRNA

KW - Biofuels

KW - Halophiles

KW - Metagenomes

KW - Microbial communities

KW - RNA 16S

KW - starch

KW - water

KW - amino acid metabolism

KW - Article

KW - chemical analysis

KW - DNA extraction

KW - enzyme activity

KW - gene sequence

KW - hypersaline gradient

KW - metagenome

KW - methanogenesis

KW - microbial community

KW - microbiological parameters

KW - nonhuman

KW - open reading frame

KW - salinity

KW - sediment

KW - 16S rRNA

KW - Biofuels

KW - Halophiles

KW - Metagenomes

KW - Microbial communities

U2 - 10.3389/fmicb.2018.01492

DO - 10.3389/fmicb.2018.01492

M3 - Article

VL - 9

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - JUL

ER -