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Rasmussen AN, Damashek J, Eloe-Fadrosh EA, Francis CA. In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay. MICROBIAL ECOLOGY 2021; 81:601-616. [PMID: 33150499 DOI: 10.1007/s00248-020-01621-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA
| | - Julian Damashek
- Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA
- Department of Biology, Utica College, Utica, NY, 13502, USA
| | - Emiley A Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, 473 Via Ortega, Y2E2 Bldg Rm 140, Stanford, CA, 94305, USA.
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Pinto OHB, Silva TF, Vizzotto CS, Santana RH, Lopes FAC, Silva BS, Thompson FL, Kruger RH. Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume. BMC Microbiol 2020; 20:13. [PMID: 31941452 PMCID: PMC6964070 DOI: 10.1186/s12866-020-1698-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 11/15/2022] Open
Abstract
Background Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.
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Affiliation(s)
- Otávio H B Pinto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Thais F Silva
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil
| | - Carla S Vizzotto
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.,Department of Civil and Environmental Engineering, University of Brasília, Brasilia, 70910-900, Brazil
| | | | - Fabyano A C Lopes
- Laboratory of Microbiology, Federal University of Tocantins, Palmas, 77500-000, Brazil
| | - Bruno S Silva
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Fabiano L Thompson
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
| | - Ricardo H Kruger
- Department of Enzymology, Institute of Biological Sciences, University of Brasília, Brasilia, 70910-900, Brazil.
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Alfreider A, Grimus V, Luger M, Ekblad A, Salcher MM, Summerer M. Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes. FEMS Microbiol Ecol 2019; 94:5076030. [PMID: 30137292 PMCID: PMC6118323 DOI: 10.1093/femsec/fiy163] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/02/2022] Open
Abstract
Niche specialization of nitrifying prokaryotes is usually studied with tools targeting molecules involved in the oxidation of ammonia and nitrite. The ecological significance of diverse CO2 fixation strategies used by nitrifiers is, however, mostly unexplored. By analyzing autotrophy-related genes in combination with amoA marker genes based on droplet digitial PCR and CARD-FISH counts targeting rRNA, we quantified the distribution of nitrifiers in eight stratified lakes. Ammonia oxidizing (AO) Thaumarchaeota using the 3-hydroxypropionate/4-hydroxybutyrate pathway dominated deep and oligotrophic lakes, whereas Nitrosomonas-related taxa employing the Calvin cycle were important AO bacteria in smaller lakes. The occurrence of nitrite oxidizing Nitrospira, assimilating CO2 with the reductive TCA cycle, was strongly correlated with the distribution of Thaumarchaeota. Recently discovered complete ammonia-oxidizing bacteria (comammox) belonging to Nitrospira accounted only for a very small fraction of ammonia oxidizers (AOs) present at the study sites. Altogether, this study gives a first insight on how physicochemical characteristics in lakes are associated to the distribution of nitrifying prokaryotes with different CO2 fixation strategies. Our investigations also evaluate the suitability of functional genes associated with individual CO2 assimilation pathways to study niche preferences of different guilds of nitrifying microorganisms based on an autotrophic perspective.
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Affiliation(s)
- Albin Alfreider
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Victoria Grimus
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Martin Luger
- Institute for Water Ecology, Fisheries Biology and Lake Research, Federal Agency for Water Management, Scharfling 18, 5310 Mondsee, Austria
| | - Anja Ekblad
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Na Sádkách, 702/7370 05 Ceské Budejovice, Czech Republic
| | - Monika Summerer
- Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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Techtman SM, Mahmoudi N, Whitt KT, Campa MF, Fortney JL, Joyner DC, Hazen TC. Comparison of Thaumarchaeotal populations from four deep sea basins. FEMS Microbiol Ecol 2018; 93:4331633. [PMID: 29029137 PMCID: PMC5812500 DOI: 10.1093/femsec/fix128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 09/29/2017] [Indexed: 11/13/2022] Open
Abstract
The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. These findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.
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Affiliation(s)
- Stephen M Techtman
- Department of Biological Sciences, Michigan Technological University, Houghton MI 49931-1295, USA
| | - Nagissa Mahmoudi
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Kendall T Whitt
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Maria Fernanda Campa
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA
| | - Julian L Fortney
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Dominique C Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.,Bredesen Center, University of Tennessee, Knoxville, TN 37996, USA.,Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN 37916, USA.,Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN 37996, USA
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Wang Y, Zhang R, He Z, Van Nostrand JD, Zheng Q, Zhou J, Jiao N. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment. Front Microbiol 2017; 8:1153. [PMID: 28680420 PMCID: PMC5478683 DOI: 10.3389/fmicb.2017.01153] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 06/07/2017] [Indexed: 01/28/2023] Open
Abstract
Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C), nitrogen (N), and phosphorus (P) cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS) is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip), we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D)] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT) showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH), transformation of hydroxylamine to nitrite (hao) and ammonification (gdh) genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated with salinity, temperature, and chlorophyll based on canonical correspondence analysis, suggesting a significant influence of hydrologic conditions on water microbial communities. Our data provide new insights into better understanding of the functional potential of microbial communities in the complex estuarine-coastal environmental gradient of the ECS.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Zhili He
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Institute for Energy and the Environment and Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, BerkeleyCA, United States.,School of Environment, Tsinghua UniversityBeijing, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen UniversityXiamen, China.,Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
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Alfreider A, Baumer A, Bogensperger T, Posch T, Salcher MM, Summerer M. CO 2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs. Environ Microbiol 2017; 19:2754-2768. [PMID: 28474482 PMCID: PMC5619642 DOI: 10.1111/1462-2920.13786] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 11/23/2022]
Abstract
While mechanisms of different carbon dioxide (CO2) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO2 fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO2 fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.
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Affiliation(s)
- Albin Alfreider
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andreas Baumer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
| | | | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Michaela M Salcher
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Monika Summerer
- Institute for Ecology, University of Innsbruck, Innsbruck, Austria
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