1
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Gill JG, Hill-Spanik KM, Whittaker KA, Jones ML, Plante C. Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 2022; 10:e12835. [PMID: 35251777 PMCID: PMC8893026 DOI: 10.7717/peerj.12835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
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Affiliation(s)
- John Geoffrey Gill
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | | | - Kerry A. Whittaker
- Sea Education Association, Woods Hole, MA, United States,Maine Maritime Academy, Castine, Maine, United States
| | - Martin L. Jones
- Department of Mathematics, College of Charleston, Charleston, SC, United States
| | - Craig Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
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2
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Wang Y, Liao S, Gai Y, Liu G, Jin T, Liu H, Gram L, Strube ML, Fan G, Sahu SK, Liu S, Gan S, Xie Z, Kong L, Zhang P, Liu X, Wang DZ. Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean. Front Microbiol 2021; 12:518865. [PMID: 33679623 PMCID: PMC7935530 DOI: 10.3389/fmicb.2021.518865] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/25/2021] [Indexed: 11/19/2022] Open
Abstract
Despite being the world’s third largest ocean, the Indian Ocean is one of the least studied and understood with respect to microbial diversity as well as biogeochemical and ecological functions. In this study, we investigated the microbial community and its metabolic potential for nitrogen (N) acquisition in the oligotrophic surface waters of the Indian Ocean using a metagenomic approach. Proteobacteria and Cyanobacteria dominated the microbial community with an average 37.85 and 23.56% of relative abundance, respectively, followed by Bacteroidetes (3.73%), Actinobacteria (1.69%), Firmicutes (0.76%), Verrucomicrobia (0.36%), and Planctomycetes (0.31%). Overall, only 24.3% of functional genes were common among all sampling stations indicating a high level of gene diversity. However, the presence of 82.6% common KEGG Orthology (KOs) in all samples showed high functional redundancy across the Indian Ocean. Temperature, phosphate, silicate and pH were important environmental factors regulating the microbial distribution in the Indian Ocean. The cyanobacterial genus Prochlorococcus was abundant with an average 17.4% of relative abundance in the surface waters, and while 54 Prochlorococcus genomes were detected, 53 were grouped mainly within HLII clade. In total, 179 of 234 Prochlorococcus sequences extracted from the global ocean dataset were clustered into HL clades and exhibited less divergence, but 55 sequences of LL clades presented more divergence exhibiting different branch length. The genes encoding enzymes related to ammonia metabolism, such as urease, glutamate dehydrogenase, ammonia transporter, and nitrilase presented higher abundances than the genes involved in inorganic N assimilation in both microbial community and metagenomic Prochlorococcus population. Furthermore, genes associated with dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification and anammox were absent in metagenome Prochlorococcus population, i.e., nitrogenase and nitrate reductase. Notably, the de novo biosynthesis pathways of six different amino acids were incomplete in the metagenomic Prochlorococcus population and Prochlorococcus genomes, suggesting compensatory uptake of these amino acids from the environment. These results reveal the features of the taxonomic and functional structure of the Indian Ocean microbiome and their adaptive strategies to ambient N deficiency in the oligotrophic ocean.
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Affiliation(s)
- Yayu Wang
- BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Shuilin Liao
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Beijing, China
| | - Yingbao Gai
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Tao Jin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Zhangxian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lingfen Kong
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
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3
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Di Cesare A, Dzhembekova N, Cabello-Yeves PJ, Eckert EM, Slabakova V, Slabakova N, Peneva E, Bertoni R, Corno G, Salcher MM, Kamburska L, Bertoni F, Rodriguez-Valera F, Moncheva S, Callieri C. Genomic Comparison and Spatial Distribution of Different Synechococcus Phylotypes in the Black Sea. Front Microbiol 2020; 11:1979. [PMID: 32903389 PMCID: PMC7434838 DOI: 10.3389/fmicb.2020.01979] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/27/2020] [Indexed: 11/24/2022] Open
Abstract
Picocyanobacteria of the genus Synechococcus are major contributors to global primary production and nutrient cycles due to their oxygenic photoautotrophy, their abundance, and the extensive distribution made possible by their wide-ranging biochemical capabilities. The recent recovery and isolation of strains from the deep euxinic waters of the Black Sea encouraged us to expand our analysis of their adaptability also beyond the photic zone of aquatic environments. To this end, we quantified the total abundance and distribution of Synechococcus along the whole vertical profile of the Black Sea by flow cytometry, and analyzed the data obtained in light of key environmental factors. Furthermore, we designed phylotype-specific primers using the genomes of two new epipelagic coastal strains – first described here – and of two previously described mesopelagic strains, analyzed their presence/abundance by qPCR, and tested this parameter also in metagenomes from two stations at different depths. Together, whole genome sequencing, metagenomics and qPCR techniques provide us with a higher resolution of Synechococcus dynamics in the Black Sea. Both phylotypes analyzed are abundant and successful in epipelagic coastal waters; but while the newly described epipelagic strains are specifically adapted to this environment, the strains previously isolated in mesopelagic waters are able, in low numbers, to withstand the aphotic and oxygen depleted conditions of deep layers. This heterogeneity allows different Synechococcus phylotypes to occupy different niches and underscores the importance of a more detailed characterization of the abundance, distribution, and dynamics of individual populations of these picocyanobacteria.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Nina Dzhembekova
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Ester M Eckert
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Violeta Slabakova
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Nataliya Slabakova
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Elisaveta Peneva
- Faculty of Physics, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Roberto Bertoni
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Gianluca Corno
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | - Michaela M Salcher
- Biology Centre Czech Academy of Science (CAS), Institute of Hydrobiology, Czechia
| | - Lyudmila Kamburska
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
| | | | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain.,Laboratory for Theoretical and Computer Studies of Biological Macromolecules and Genomes, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Snejana Moncheva
- Institute of Oceanology "Fridtjof Nansen" - Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Cristiana Callieri
- National Research Council (CNR), Institute of Water Research (IRSA), Verbania, Italy
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4
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Eduardo-Correia B, Morales-Filloy H, Abad JP. Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players. Front Microbiol 2020; 10:3071. [PMID: 31998281 PMCID: PMC6965355 DOI: 10.3389/fmicb.2019.03071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs CzR/TcR in Betaproteobacteria, and CcR/TcR and EmR/SmR in Sphingobacteriia at the class level, while at the genus level, was found for CcR/TcR and NxR/TmR in Mesonia, CzR/TmR and EmR/KmR in Paenibacillus, and CcR/EmR and RpR/TcR in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.
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Affiliation(s)
- Benedito Eduardo-Correia
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - Héctor Morales-Filloy
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - José P Abad
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
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5
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Tkacz A, Hortala M, Poole PS. Absolute quantitation of microbiota abundance in environmental samples. MICROBIOME 2018; 6:110. [PMID: 29921326 PMCID: PMC6009823 DOI: 10.1186/s40168-018-0491-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/30/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Microbial communities (microbiota) influence human and animal disease and immunity, geochemical nutrient cycling and plant productivity. Specific groups, including bacteria, archaea, eukaryotes or fungi, are amplified by PCR to assess the relative abundance of sub-groups (e.g. genera). However, neither the absolute abundance of sub-groups is revealed, nor can different amplicon families (i.e. OTUs derived from a specific pair of PCR primers such as bacterial 16S, eukaryotic 18S or fungi ITS) be compared. This prevents determination of the absolute abundance of a particular group and domain-level shifts in microbiota abundance can remain undetected. RESULTS We have developed absolute quantitation of amplicon families using synthetic chimeric DNA spikes. Synthetic spikes were added directly to environmental samples, co-isolated and PCR-amplified, allowing calculation of the absolute abundance of amplicon families (e.g. prokaryotic 16S, eukaryotic 18S and fungal ITS per unit mass of sample). CONCLUSIONS Spikes can be adapted to any amplicon-specific group including rhizobia from soils, Firmicutes and Bifidobacteria from human gut or Enterobacteriaceae from food samples. Crucially, using highly complex soil samples, we show that the absolute abundance of specific groups can remain steady or increase, even when their relative abundance decreases. Thus, without absolute quantitation, the underlying pathology, physiology and ecology of microbial groups may be masked by their relative abundance.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Marion Hortala
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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6
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Dubinsky V, Haber M, Burgsdorf I, Saurav K, Lehahn Y, Malik A, Sher D, Aharonovich D, Steindler L. Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea. Environ Microbiol 2017; 19:1077-1090. [DOI: 10.1111/1462-2920.13624] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Vadim Dubinsky
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Yoav Lehahn
- Department of Earth and Planetary Sciences; Weizmann Institute of Science; Rehovot Israel
| | - Assaf Malik
- Bioinformatics Service Unit, University of Haifa; Haifa Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences; University of Haifa; Haifa Israel
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7
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Guerrero-Feijóo E, Nieto-Cid M, Sintes E, Dobal-Amador V, Hernando-Morales V, Álvarez M, Balagué V, Varela MM. Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the North Atlantic Ocean. FEMS Microbiol Ecol 2016; 93:fiw224. [PMID: 27789536 DOI: 10.1093/femsec/fiw224] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/19/2016] [Accepted: 10/25/2016] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic abundance, activity and community composition were studied in the euphotic, intermediate and deep waters off the Galician coast (NW Iberian margin) in relation to the optical characterization of dissolved organic matter (DOM). Microbial (archaeal and bacterial) community structure was vertically stratified. Among the Archaea, Euryarchaeota, especially Thermoplasmata, was dominant in the intermediate waters and decreased with depth, whereas marine Thaumarchaeota, especially Marine Group I, was the most abundant archaeal phylum in the deeper layers. The bacterial community was dominated by Proteobacteria through the whole water column. However, Cyanobacteria and Bacteroidetes occurrence was considerable in the upper layer and SAR202 was dominant in deep waters. Microbial composition and abundance were not shaped by the quantity of dissolved organic carbon, but instead they revealed a strong connection with the DOM quality. Archaeal communities were mainly related to the fluorescence of DOM (which indicates respiration of labile DOM and generation of refractory subproducts), while bacterial communities were mainly linked to the aromaticity/age of the DOM produced along the water column. Taken together, our results indicate that the microbial community composition is associated with the DOM composition of the water masses, suggesting that distinct microbial taxa have the potential to use and/or produce specific DOM compounds.
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Affiliation(s)
- Elisa Guerrero-Feijóo
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain
| | - Mar Nieto-Cid
- IIM-CSIC, Instituto de Investigacións Mariñas, 36208 Vigo, Spain
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, A-1090, Vienna, Austria
| | - Vladimir Dobal-Amador
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain.,Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, 36200 Vigo, Spain
| | | | - Marta Álvarez
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain
| | - Vanessa Balagué
- ICM-CSIC, Institut de Ciències del Mar, 08003, Barcelona, Spain
| | - Marta M Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo. 130, 15080, A Coruña, Spain
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8
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Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y, Schäfer H. A mechanism for bacterial transformation of dimethylsulfide to dimethylsulfoxide: a missing link in the marine organic sulfur cycle. Environ Microbiol 2016; 18:2754-66. [PMID: 27114231 DOI: 10.1111/1462-2920.13354] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/19/2016] [Indexed: 11/30/2022]
Abstract
The volatile organosulfur compound, dimethylsulfide (DMS), plays an important role in climate regulation and global sulfur biogeochemical cycles. Microbial oxidation of DMS to dimethylsulfoxide (DMSO) represents a major sink of DMS in surface seawater, yet the underlying molecular mechanisms and key microbial taxa involved are not known. Here, we reveal that Ruegeria pomeroyi, a model marine heterotrophic bacterium, can oxidize DMS to DMSO using trimethylamine monooxygenase (Tmm). Purified Tmm oxidizes DMS to DMSO at a 1:1 ratio. Mutagenesis of the tmm gene in R. pomeroyi completely abolished DMS oxidation and subsequent DMSO formation. Expression of Tmm and DMS oxidation in R. pomeroyi is methylamine-dependent and regulated at the post-transcriptional level. Considering that Tmm is present in approximately 20% of bacterial cells inhabiting marine surface waters, particularly the marine Roseobacter clade and the SAR11 clade, our observations contribute to a mechanistic understanding of biological DMSO production in surface seawater.
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Affiliation(s)
- Ian Lidbury
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Eileen Kröber
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agriculture Sciences, Urumqi, 830091, China
| | - Yijun Zhu
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK
| | - Yin Chen
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Hendrik Schäfer
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
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9
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Larkin AA, Blinebry SK, Howes C, Lin Y, Loftus SE, Schmaus CA, Zinser ER, Johnson ZI. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific. ISME JOURNAL 2016; 10:1555-67. [PMID: 26800235 DOI: 10.1038/ismej.2015.244] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/30/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023]
Abstract
The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some 'sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.
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Affiliation(s)
- Alyse A Larkin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sara K Blinebry
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Caroline Howes
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Yajuan Lin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sarah E Loftus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Carrie A Schmaus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zackary I Johnson
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
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10
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Gutiérrez MH, Galand PE, Moffat C, Pantoja S. Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord. Environ Microbiol 2015; 17:3882-97. [PMID: 25856307 DOI: 10.1111/1462-2920.12872] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 01/30/2023]
Abstract
Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.
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Affiliation(s)
- Marcelo H Gutiérrez
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
| | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, F-66650, Banyuls sur Mer, France
| | - Carlos Moffat
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile.,Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Silvio Pantoja
- Department of Oceanography, Universidad de Concepción, Concepción, Chile.,COPAS Sur-Austral Program, Universidad de Concepción, Concepción, Chile
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