1
|
Masuda T, Inomura K, Kodama T, Shiozaki T, Kitajima S, Armin G, Matsui T, Suzuki K, Takeda S, Sato M, Prášil O, Furuya K. Crocosphaera as a Major Consumer of Fixed Nitrogen. Microbiol Spectr 2022; 10:e0217721. [PMID: 35770981 PMCID: PMC9431459 DOI: 10.1128/spectrum.02177-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/05/2022] [Indexed: 11/23/2022] Open
Abstract
Crocosphaera watsonii (hereafter referred to as Crocosphaera) is a key nitrogen (N) fixer in the ocean, but its ability to consume combined-N sources is still unclear. Using in situ microcosm incubations with an ecological model, we show that Crocosphaera has high competitive capability both under low and moderately high combined-N concentrations. In field incubations, Crocosphaera accounted for the highest consumption of ammonium and nitrate, followed by picoeukaryotes. The model analysis shows that cells have a high ammonium uptake rate (~7 mol N [mol N]-1 d-1 at the maximum), which allows them to compete against picoeukaryotes and nondiazotrophic cyanobacteria when combined N is sufficiently available. Even when combined N is depleted, their capability of nitrogen fixation allows higher growth rates compared to potential competitors. These results suggest the high fitness of Crocosphaera in combined-N limiting, oligotrophic oceans heightening its potential significance in its ecosystem and in biogeochemical cycling. IMPORTANCE Crocosphaera watsonii is as a key nitrogen (N) supplier in marine ecosystems, and it has been estimated to contribute up to half of oceanic N2 fixation. Conversely, a recent study reported that Crocosphaera can assimilate combined N and proposed that unicellular diazotrophs can be competitors with non-N2 fixing phytoplankton for combined N. Despite its importance in nitrogen cycling, the methods by which Crocosphaera compete are not currently fully understood. Here, we present a new role of Crocosphaera as a combined-N consumer: a competitor against nondiazotrophic phytoplankton for combined N. In this study, we combined in situ microcosm experiments and an ecosystem model to quantitatively evaluate the combined-N consumption by Crocosphaera and other non-N2 fixing phytoplankton. Our results suggest the high fitness of Crocosphaera in combined-N limiting, oligotrophic oceans and, thus, heightens its potential significance in its ecosystem and in biogeochemical cycling.
Collapse
Affiliation(s)
- Takako Masuda
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Taketoshi Kodama
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Takuhei Shiozaki
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Satoshi Kitajima
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Takato Matsui
- Graduate School of Environmental Science/Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Koji Suzuki
- Graduate School of Environmental Science/Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Shigenobu Takeda
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Mitsuhide Sato
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czech Republic
| | - Ken Furuya
- Department of Aquatic Bioscience, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
2
|
Coyne KJ, Parker AE, Lee CK, Sohm JA, Kalmbach A, Gunderson T, León-Zayas R, Capone DG, Carpenter EJ, Cary SC. The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2020; 96:5714082. [PMID: 31967635 PMCID: PMC7043275 DOI: 10.1093/femsec/fiaa010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
Collapse
Affiliation(s)
- Kathryn J Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Alexander E Parker
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Jill A Sohm
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Andrew Kalmbach
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Troy Gunderson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Rosa León-Zayas
- Willamette University, Biology Department, Salem, OR 97301, USA
| | - Douglas G Capone
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Edward J Carpenter
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - S Craig Cary
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
| |
Collapse
|
3
|
Yang QS, Dong JD, Ahmad M, Ling J, Zhou WG, Tan YH, Zhang YZ, Shen DD, Zhang YY. Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs. BMC Microbiol 2019; 19:188. [PMID: 31416417 PMCID: PMC6694519 DOI: 10.1186/s12866-019-1565-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea. RESULTS The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high. CONCLUSIONS The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.
Collapse
Affiliation(s)
- Qing-Song Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-De Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China
| | - Manzoor Ahmad
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wei-Guo Zhou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye-Hui Tan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yuan-Zhou Zhang
- State Oceanic Administration Sansha Marine Environmental Monitoring Center Station, Haikou, 570311, China
| | - Dan-Dan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, 18119, Warnemünde, Germany.
| | - Yan-Ying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, 572000, China.
| |
Collapse
|
4
|
Luo YW, Shi D, Kranz SA, Hopkinson BM, Hong H, Shen R, Zhang F. Reduced nitrogenase efficiency dominates response of the globally important nitrogen fixer Trichodesmium to ocean acidification. Nat Commun 2019; 10:1521. [PMID: 30944323 PMCID: PMC6447586 DOI: 10.1038/s41467-019-09554-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
The response of the prominent marine dinitrogen (N2)-fixing cyanobacteria Trichodesmium to ocean acidification (OA) is critical to understanding future oceanic biogeochemical cycles. Recent studies have reported conflicting findings on the effect of OA on growth and N2 fixation of Trichodesmium. Here, we quantitatively analyzed experimental data on how Trichodesmium reallocated intracellular iron and energy among key cellular processes in response to OA, and integrated the findings to construct an optimality-based cellular model. The model results indicate that Trichodesmium growth rate decreases under OA primarily due to reduced nitrogenase efficiency. The downregulation of the carbon dioxide (CO2)-concentrating mechanism under OA has little impact on Trichodesmium, and the energy demand of anti-stress responses to OA has a moderate negative effect. We predict that if anthropogenic CO2 emissions continue to rise, OA could reduce global N2 fixation potential of Trichodesmium by 27% in this century, with the largest decrease in iron-limiting regions.
Collapse
Affiliation(s)
- Ya-Wei Luo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Science and College of the Environment and Ecology, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Sven A Kranz
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Brian M Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Haizheng Hong
- State Key Laboratory of Marine Environmental Science and College of the Environment and Ecology, Xiamen University, 361102, Xiamen, Fujian, China
| | - Rong Shen
- State Key Laboratory of Marine Environmental Science and College of the Environment and Ecology, Xiamen University, 361102, Xiamen, Fujian, China
| | - Futing Zhang
- State Key Laboratory of Marine Environmental Science and College of the Environment and Ecology, Xiamen University, 361102, Xiamen, Fujian, China
| |
Collapse
|
5
|
Hong H, Shen R, Zhang F, Wen Z, Chang S, Lin W, Kranz SA, Luo YW, Kao SJ, Morel FMM, Shi D. The complex effects of ocean acidification on the prominent N2-fixing cyanobacteriumTrichodesmium. Science 2017; 356:527-531. [DOI: 10.1126/science.aal2981] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/12/2017] [Indexed: 11/02/2022]
|
6
|
Scavotto RE, Dziallas C, Bentzon-Tilia M, Riemann L, Moisander PH. Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean. Environ Microbiol 2015; 17:3754-65. [PMID: 25655773 DOI: 10.1111/1462-2920.12777] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 01/06/2015] [Accepted: 01/06/2015] [Indexed: 11/30/2022]
Abstract
The community composition of N2 -fixing microorganisms (diazotrophs) was investigated in copepods (primarily Acartia spp.) in parallel to that of seawater in coastal waters off Denmark (Øresund) and New England, USA. The unicellular cyanobacterial diazotroph UCYN-A was detected from seawater and full-gut copepods, suggesting that the new N contributed by UCYN-A is directly transferred to higher trophic levels in these waters. Deltaproteobacterial and Cluster 3 nifH sequences were detected in > 1 μm seawater particles and full-gut copepods, suggesting that they associate with copepods primarily via feeding. The dominant communities in starved copepods were Vibrio spp. and related Gammaproteobacteria, suggesting they represent the most permanent diazotroph associations in the copepods. N2 fixation rates were up to 3.02 pmol N copepod(-1) day(-1). Although at a typical copepod density in estuarine waters, these volumetric rates are low; considering the small size of a copepod, these mesozooplanktonic crustaceans may serve as hotspots of N2 fixation, at 12.9-71.9 μmol N dm(-3) copepod biomass day(-1). Taken together, diazotroph associations range from more permanent attachments to copepod feeding on some groups. Similar diazotroph groups detected on the eastern and western Atlantic Ocean suggest that these associations are a general phenomenon and play a role in the coastal N cycles.
Collapse
Affiliation(s)
- Rosemary E Scavotto
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA, 02747, USA
| | - Claudia Dziallas
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Lasse Riemann
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, DK-3000, Helsingør, Denmark
| | - Pia H Moisander
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA, 02747, USA
| |
Collapse
|
7
|
Moisander PH, Serros T, Paerl RW, Beinart RA, Zehr JP. Gammaproteobacterial diazotrophs and nifH gene expression in surface waters of the South Pacific Ocean. THE ISME JOURNAL 2014; 8:1962-73. [PMID: 24722632 PMCID: PMC4184014 DOI: 10.1038/ismej.2014.49] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 02/07/2014] [Accepted: 02/24/2014] [Indexed: 01/30/2023]
Abstract
In addition to the cyanobacterial N2-fixers (diazotrophs), there is a high nifH gene diversity of non-cyanobacterial groups present in marine environments, yet quantitative information about these groups is scarce. N2 fixation potential (nifH gene expression), diversity and distributions of the uncultivated diazotroph phylotype γ-24774A11, a putative gammaproteobacterium, were investigated in the western South Pacific Ocean. γ-24774A11 gene copies correlated positively with diazotrophic cyanobacteria, temperature, dissolved organic carbon and ambient O2 saturation, and negatively with depth, chlorophyll a and nutrients, suggesting that carbon supply, access to light or inhibitory effects of DIN may control γ-24774A11 abundances. Maximum nifH gene-copy abundance was 2 × 10(4) l(-1), two orders of magnitude less than that for diazotrophic cyanobacteria, while the median γ-24774A11 abundance, 8 × 10(2) l(-1), was greater than that for the UCYN-A cyanobacteria, suggesting a more homogeneous distribution in surface waters. The abundance of nifH transcripts by γ-24774A11 was greater during the night than during the day, and the transcripts generally ranged from 0-7%, but were up to 26% of all nifH transcripts at each station. The ubiquitous presence and low variability of γ-24774A11 abundances across tropical and subtropical oceans, combined with the consistent nifH expression reported in this study, suggest that γ-24774A11 could be one of the most important heterotrophic (or photoheterotrophic) diazotrophs and may need to be considered in future N budget estimates and models.
Collapse
Affiliation(s)
- Pia H Moisander
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Tracy Serros
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ryan W Paerl
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Roxanne A Beinart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA
| |
Collapse
|
8
|
Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria. ISME JOURNAL 2014; 8:2530-42. [PMID: 25226029 DOI: 10.1038/ismej.2014.167] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/05/2014] [Accepted: 08/08/2014] [Indexed: 11/08/2022]
Abstract
Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed 'diazotrophs') are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusually reduced genome and symbiosis with a single-celled prymnesiophyte alga. Recently a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography pier. We analyzed the metagenome of this UCYN-A2 population by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A (here called UCYN-A1) and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A1 protein-coding genes (96.6%) with high synteny, yet the average amino-acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped at the same functional and ecological level. Our results suggest that UCYN-A1 and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.
Collapse
|
9
|
Bombar D, Turk-Kubo KA, Robidart J, Carter BJ, Zehr JP. Non-cyanobacterial nifH phylotypes in the North Pacific Subtropical Gyre detected by flow-cytometry cell sorting. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:705-715. [PMID: 24115621 DOI: 10.1111/1758-2229.12070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 04/26/2013] [Accepted: 05/05/2013] [Indexed: 06/02/2023]
Abstract
In contrast to cyanobacteria, the significance of bacteria and archaea in oceanic N2 fixation remains unknown, apart from the knowledge that their nitrogenase (nifH) genes are diverse, present in all oceans and at least occasionally expressed. Non-cyanobacterial nifH sequences often occur as contamination from reagents and other sources, complicating the detection and interpretation of environmental phylotypes. We amplified and sequenced partial nifH gene fragments directly from cell populations sorted by fluorescence activated cell sorting from water collected in the North Pacific Subtropical Gyre (NPSG). Sequences recovered (195 total) included presumed heterotrophic or photoheterotrophic non-cyanobacterial nifH phylotypes previously unreported in the NPSG. A nifH sequence previously found in the South Pacific Gyre (HM210397) was exclusively recovered from sorted picoeukaryote populations, and was detected in water column samples using quantitative PCR (qPCR), with 60% of samples detected in the > 10 μm size fraction in addition to the 0.2-10 μm size fraction. A novel cluster 3-like nifH sequence was also recovered from discrete cell sorts and detected by qPCR in environmental samples. This approach enables the detection of rare nifH phylotypes, identifies possible associations with larger cells or particles and offers a possible solution for distinguishing reagent contaminants from real microbial community components.
Collapse
Affiliation(s)
- Deniz Bombar
- Ocean Sciences Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | | | | | | | | |
Collapse
|
10
|
Zhang Y, Zhao Z, Sun J, Jiao N. Diversity and distribution of diazotrophic communities in the South China Sea deep basin with mesoscale cyclonic eddy perturbations. FEMS Microbiol Ecol 2011; 78:417-27. [PMID: 22066702 DOI: 10.1111/j.1574-6941.2011.01174.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/16/2011] [Accepted: 07/14/2011] [Indexed: 11/28/2022] Open
Abstract
The South China Sea (SCS) is an oligotrophic subtropical marginal ocean with a deep basin and a permanently stratified central gyre. Upwelling and nitrogen fixation provide new nitrogen for primary production in the SCS. This study was aimed at an investigation of phylogenetic diversity and quantification of the diazotroph community in the SCS deep basin, which is characterized by frequent mesoscale eddies. The diazotroph community had a relatively low diversity but a distinct spatial heterogeneity of diversity in the SCS deep basin. The potential for nitrogen fixation consistently occurred during cyclonic eddies, although upwelling of nutrient-replete deep water might have alleviated nitrogen limitation in the SCS. However, diazotrophic proteobacteria were dominant, but neither Trichodesmium nor heterocystous cyanobacterial diatom symbionts. Quantitative PCR analysis using probe-primer sets developed in this study revealed that the nif H gene of the two dominant alpha- and gammaproteobacterial groups was at the highest abundance (up to 10(4) to 10(5) copies L(-1) ). Trichodesmium thiebautii was detected with an average density of 10(2) trichomes L(-1) in the euphotic waters, while Richelia intracellularis was observed sporadically under the microscope. The unicellular cyanobacterial groups A and B were not detected in our libraries. Our results suggested that diazotrophic proteobacteria were significant components potentially contributing to nitrogen fixation in this oligotrophic marginal ocean ecosystem.
Collapse
Affiliation(s)
- Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, China.
| | | | | | | |
Collapse
|
11
|
Preston CM, Harris A, Ryan JP, Roman B, Marin R, Jensen S, Everlove C, Birch J, Dzenitis JM, Pargett D, Adachi M, Turk K, Zehr JP, Scholin CA. Underwater application of quantitative PCR on an ocean mooring. PLoS One 2011; 6:e22522. [PMID: 21829630 PMCID: PMC3148215 DOI: 10.1371/journal.pone.0022522] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 06/22/2011] [Indexed: 11/21/2022] Open
Abstract
The Environmental Sample Processor (ESP) is a device that allows for the underwater, autonomous application of DNA and protein probe array technologies as a means to remotely identify and quantify, in situ, marine microorganisms and substances they produce. Here, we added functionality to the ESP through the development and incorporation of a module capable of solid-phase nucleic acid extraction and quantitative PCR (qPCR). Samples collected by the instrument were homogenized in a chaotropic buffer compatible with direct detection of ribosomal RNA (rRNA) and nucleic acid purification. From a single sample, both an rRNA community profile and select gene abundances were ascertained. To illustrate this functionality, we focused on bacterioplankton commonly found along the central coast of California and that are known to vary in accordance with different oceanic conditions. DNA probe arrays targeting rRNA revealed the presence of 16S rRNA indicative of marine crenarchaea, SAR11 and marine cyanobacteria; in parallel, qPCR was used to detect 16S rRNA genes from the former two groups and the large subunit RuBisCo gene (rbcL) from Synecchococcus. The PCR-enabled ESP was deployed on a coastal mooring in Monterey Bay for 28 days during the spring-summer upwelling season. The distributions of the targeted bacterioplankon groups were as expected, with the exception of an increase in abundance of marine crenarchaea in anomalous nitrate-rich, low-salinity waters. The unexpected co-occurrence demonstrated the utility of the ESP in detecting novel events relative to previously described distributions of particular bacterioplankton groups. The ESP can easily be configured to detect and enumerate genes and gene products from a wide range of organisms. This study demonstrated for the first time that gene abundances could be assessed autonomously, underwater in near real-time and referenced against prevailing chemical, physical and bulk biological conditions.
Collapse
Affiliation(s)
- Christina M Preston
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Diazotrophic diversity in the rhizosphere of two exotic weed plants, Prosopis juliflora and Parthenium hysterophorus. World J Microbiol Biotechnol 2011; 28:605-13. [PMID: 22806856 DOI: 10.1007/s11274-011-0853-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
Abstract
This study is aimed at assessing culturable diazotrophic bacterial diversity in the rhizosphere of Prosopis juliflora and Parthenium hysterophorus, which grow profusely in nutritionally-poor soils and environmentally-stress conditions so as to identify some novel strains for bioinoculant technology. Diazotrophic isolates from Prosopis and Parthenium rhizosphere were characterized for nitrogenase activity by Acetylene Reduction Assay (ARA) and 16S rRNA gene sequencing. Further, the culture-independent quantitative PCR (qPCR) was performed to compare the abundance of diazotrophs in rhizosphere with bulk soils. The proportion of diazotrophs in total heterotrophs was higher in rhizosphere than bulk soils and 32 putative diazotrophs from rhizosphere of two plants were identified by nifH gene amplification. The ARA activity of the isolates ranged from 40 to 95 nmol ethylene h(-1) mg protein(-1). The 16S rRNA gene analysis identified the isolates to be members of alpha, beta and gamma Proteobacteria and firmicutes. The qPCR assay also confirmed that abundance of nif gene in rhizosphere of these two plants was 10-fold higher than bulk soil.
Collapse
|
13
|
Abundance and diversity of nitrogen-fixing bacteria in rhizosphere and bulk paddy soil under different duration of organic management. World J Microbiol Biotechnol 2011; 28:493-503. [DOI: 10.1007/s11274-011-0840-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 07/04/2011] [Indexed: 10/18/2022]
|
14
|
Paerl RW, Johnson KS, Welsh RM, Worden AZ, Chavez FP, Zehr JP. Differential distributions of synechococcus subgroups across the california current system. Front Microbiol 2011; 2:59. [PMID: 21833315 PMCID: PMC3153035 DOI: 10.3389/fmicb.2011.00059] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/15/2011] [Indexed: 01/08/2023] Open
Abstract
Synechococcus is an abundant marine cyanobacterial genus composed of different populations that vary physiologically. Synechococcus narB gene sequences (encoding for nitrate reductase in cyanobacteria) obtained previously from isolates and the environment (e.g., North Pacific Gyre Station ALOHA, Hawaii or Monterey Bay, CA, USA) were used to develop quantitative PCR (qPCR) assays. These qPCR assays were used to quantify populations from specific narB phylogenetic clades across the California Current System (CCS), a region composed of dynamic zones between a coastal-upwelling zone and the oligotrophic Pacific Ocean. Targeted populations (narB subgroups) had different biogeographic patterns across the CCS, which appear to be driven by environmental conditions. Subgroups C_C1, D_C1, and D_C2 were abundant in coastal-upwelling to coastal-transition zone waters with relatively high to intermediate ammonium, nitrate, and chl. a concentrations. Subgroups A_C1 and F_C1 were most abundant in coastal-transition zone waters with intermediate nutrient concentrations. E_O1 and G_O1 were most abundant at different depths of oligotrophic open-ocean waters (either in the upper mixed layer or just below). E_O1, A_C1, and F_C1 distributions differed from other narB subgroups and likely possess unique ecologies enabling them to be most abundant in waters between coastal and open-ocean waters. Different CCS zones possessed distinct Synechococcus communities. Core California current water possessed low numbers of narB subgroups relative to counted Synechococcus cells, and coastal-transition waters contained high abundances of Synechococcus cells and total number of narB subgroups. The presented biogeographic data provides insight on the distributions and ecologies of Synechococcus present in an eastern boundary current system.
Collapse
Affiliation(s)
- Ryan W Paerl
- Department of Ocean Sciences, University of California Santa Cruz Santa Cruz, CA, USA
| | | | | | | | | | | |
Collapse
|
15
|
Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. ISME JOURNAL 2011; 5:1095-107. [PMID: 21289652 DOI: 10.1038/ismej.2010.209] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ostreococcus is a marine picophytoeukaryote for which culture studies indicate there are 'high-light' and 'low-light' adapted ecotypes. Representatives of these ecotypes fall within two to three 18S ribosomal DNA (rDNA) clades for the former and one for the latter. However, clade distributions and relationships to this form of niche partitioning are unknown in nature. We developed two quantitative PCR primer-probe sets and enumerated the proposed ecotypes in the Pacific Ocean as well as the subtropical and tropical North Atlantic. Statistical differences in factors such as salinity, temperature and NO(3) indicated the ecophysiological parameters behind clade distributions are more complex than irradiance alone. Clade OII, containing the putatively low-light adapted strains, was detected at warm oligotrophic sites. In contrast, Clade OI, containing high-light adapted strains, was present in cooler mesotrophic and coastal waters. Maximal OI abundance (19 555±37 18S rDNA copies per ml) was detected in mesotrophic waters at 40 m depth, approaching the nutricline. OII was often more abundant at the deep chlorophyll maximum, when nutrient concentrations were significantly higher than at the surface (stratified euphotic zone waters). However, in mixed euphotic-zone water columns, relatively high numbers (for example, 891±107 18S rDNA copies per ml, Sargasso Sea, springtime) were detected at the surface. Both Clades OI and OII were found at multiple euphotic zone depths, but co-occurrence at the same geographical location appeared rare and was detected only in continental slope waters. In situ growth rate estimates using these primer-probes and better comprehension of physiology will enhance ecological understanding of Ostreococcus Clades OII and OI which appear to be oceanic and coastal clades, respectively.
Collapse
|
16
|
Dekas AE, Orphan VJ. Identification of diazotrophic microorganisms in marine sediment via fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Methods Enzymol 2011; 486:281-305. [PMID: 21185440 DOI: 10.1016/b978-0-12-381294-0.00012-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study.
Collapse
Affiliation(s)
- Anne E Dekas
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | | |
Collapse
|
17
|
Bothe H, Schmitz O, Yates MG, Newton WE. Nitrogen fixation and hydrogen metabolism in cyanobacteria. Microbiol Mol Biol Rev 2010; 74:529-51. [PMID: 21119016 PMCID: PMC3008169 DOI: 10.1128/mmbr.00033-10] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N(2) fixation and/or H(2) formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H(2) as a source of combustible energy. To enhance the rates of H(2) production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H(2) formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.
Collapse
Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zülpicher Str. 47b, D-50923 Cologne, Germany.
| | | | | | | |
Collapse
|
18
|
Pennebaker K, Mackey KRM, Smith RM, Williams SB, Zehr JP. Diel cycling of DNA staining and nifH gene regulation in the unicellular cyanobacterium Crocosphaera watsonii strain WH 8501 (Cyanophyta). Environ Microbiol 2010; 12:1001-10. [PMID: 20105217 DOI: 10.1111/j.1462-2920.2010.02144.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Crocosphaera watsonii WH 8501 is a marine unicellular cyanobacterium that fixes nitrogen primarily during the dark phase of a light-dark (LD) cycle. Circadian clocks modulate gene transcription and cellular activity in many, if not all, cyanobacteria. A model for circadian control has been proposed in cyanobacteria, called the oscilloid model, which is based on topological changes of nucleoid DNA which in turn regulates gene transcription. In this study, the marine unicellular diazotrophic cyanobacteria C. watsonii WH 8501 and Cyanothece sp. ATCC 51142 were found to have daily fluctuations in DNA staining using Hoechst 33342 and SYBR I Green fluorescent dyes. Up to 20-fold decreases in DNA fluorescence of Hoechst-stained cells were observed during the dark phase when cultures were grown with a 12:12 LD cycle or under continuous light (LL). The variation in DNA staining was consistent with changes in DNA topology proposed in the oscilloid model. The abundance of nifH transcripts in C. watsonii WH 8501 was rhythmic under LD and LL cycles, consistent with a circadian rhythm. Cycles of DNA fluorescence and photosynthetic efficiency were disrupted when cultures were shifted into an early dark phase; however, nifH transcripts predictably increased in abundance following the premature transition from light to darkness. Thus, nifH gene expression in C. watsonii WH 8501 appears to be influenced by both circadian and environmental factors.
Collapse
Affiliation(s)
- Kory Pennebaker
- Ocean Sciences Department, University of California, Santa Cruz, CA 95064, USA
| | | | | | | | | |
Collapse
|
19
|
Preston CM, Marin R, Jensen SD, Feldman J, Birch JM, Massion EI, DeLong EF, Suzuki M, Wheeler K, Scholin CA. Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes. Environ Microbiol 2009; 11:1168-80. [DOI: 10.1111/j.1462-2920.2009.01848.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Moisander PH, Beinart RA, Voss M, Zehr JP. Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. ISME JOURNAL 2008; 2:954-67. [PMID: 18528417 DOI: 10.1038/ismej.2008.51] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The spatial heterogeneity of diversity and abundance of diazotrophs were investigated off the Vietnamese coast in the South China Sea (SCS). The study area extended from the Mekong River plume to the shelf region and beyond to stations extending to 1700 m depth. The SCS diazotroph community, based on nifH gene diversity, had components closely related to sequences from open ocean, estuarine, saltmarsh and microbial mat communities. Rarefaction analysis suggested that by using a 97% similarity operational taxonomic unit definition, the majority of nifH sequence diversity in the samples was covered by the 384 nifH clones obtained. The majority of the nifH sequences recovered fell into two clusters: one comprised of Trichodesmium sequences and the other an alpha-proteobacterial group. Unicellular cyanobacterial groups A and B, and symbiotic filamentous cyanobacterial diazotrophs were detected sporadically. Trichodesmium was by far the most abundant diazotroph, with up to 6 x 10(5) nifH gene copies per liter. Quantitative PCR probe-primer sets were designed and used to quantify two proteobacterial groups, revealing abundances up to 10(3)-10(4) nifH gene copies per liter, with the highest abundances in the photic zone. Major components of the clone library were also revealed by a nifH microarray and multidimensional scaling (MDS) analysis. MDS showed that samples from the >10 microm size fraction from 0- to 5-m depths clustered separately from the rest of the samples, primarily due to the abundance of Trichodesmium sequences. The SCS diazotroph community has a relatively low diversity and is a mixture of both estuarine and oceanic fingerprints.
Collapse
Affiliation(s)
- Pia H Moisander
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
| | | | | | | |
Collapse
|
21
|
Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl Environ Microbiol 2008. [PMID: 18245263 DOI: 10.1128/aem.01720‐07] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the factors that influence the distribution and abundance of marine diazotrophs is important in order to assess their role in the oceanic nitrogen cycle. Environmental DNA samples from four cruises to the North Atlantic Ocean, covering a sampling area of 0 degrees N to 42 degrees N and 67 degrees W to 13 degrees W, were analyzed for the presence and amount of seven nifH phylotypes using real-time quantitative PCR and TaqMan probes. The cyanobacterial phylotypes dominated in abundance (94% of all nifH copies detected) and were the most widely distributed. The filamentous cyanobacterial type, which included both Trichodesmium and Katagnymene, was the most abundant (51%), followed by group A, an uncultured unicellular cyanobacterium (33%), and gamma A, an uncultured gammaproteobacterium (6%). Group B, unicellular cyanobacterium Crocosphaera, and group C Cyanothece-like phylotypes were not often detected (6.9% and 2.3%, respectively), but where present, could reach high concentrations. Gamma P, another uncultured gammaproteobacterium, was seldom detected (0.5%). Water temperature appeared to influence the distribution of many nifH phylotypes. Very high (up to 1 x 10(6) copies liter(-1)) nifH concentrations of group A were detected in the eastern basin (25 to 17 degrees N, 27 to 30 degrees W), where the temperature ranged from 20 to 23 degrees C. The highest concentrations of filamentous phylotypes were measured between 25 and 30 degrees C. The uncultured cluster III phylotype was uncommon (0.4%) and was associated with mean water temperatures of 18 degrees C. Diazotroph abundance was highest in regions where modeled average dust deposition was between 1 and 2 g/m(2)/year.
Collapse
|
22
|
Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean. Appl Environ Microbiol 2008; 74:1922-31. [PMID: 18245263 DOI: 10.1128/aem.01720-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the factors that influence the distribution and abundance of marine diazotrophs is important in order to assess their role in the oceanic nitrogen cycle. Environmental DNA samples from four cruises to the North Atlantic Ocean, covering a sampling area of 0 degrees N to 42 degrees N and 67 degrees W to 13 degrees W, were analyzed for the presence and amount of seven nifH phylotypes using real-time quantitative PCR and TaqMan probes. The cyanobacterial phylotypes dominated in abundance (94% of all nifH copies detected) and were the most widely distributed. The filamentous cyanobacterial type, which included both Trichodesmium and Katagnymene, was the most abundant (51%), followed by group A, an uncultured unicellular cyanobacterium (33%), and gamma A, an uncultured gammaproteobacterium (6%). Group B, unicellular cyanobacterium Crocosphaera, and group C Cyanothece-like phylotypes were not often detected (6.9% and 2.3%, respectively), but where present, could reach high concentrations. Gamma P, another uncultured gammaproteobacterium, was seldom detected (0.5%). Water temperature appeared to influence the distribution of many nifH phylotypes. Very high (up to 1 x 10(6) copies liter(-1)) nifH concentrations of group A were detected in the eastern basin (25 to 17 degrees N, 27 to 30 degrees W), where the temperature ranged from 20 to 23 degrees C. The highest concentrations of filamentous phylotypes were measured between 25 and 30 degrees C. The uncultured cluster III phylotype was uncommon (0.4%) and was associated with mean water temperatures of 18 degrees C. Diazotroph abundance was highest in regions where modeled average dust deposition was between 1 and 2 g/m(2)/year.
Collapse
|
23
|
Abstract
Like many estuaries, the Chesapeake Bay has pronounced gradients in salinity and nutrients. Previous studies have shown that there is a high diversity of nitrogenase (nifH) genes in the estuary, and that there are specific distributions of individual nifH phylotypes. In contrast to previous work that revealed the remarkable diversity of nifH phylotypes in the Chesapeake estuary, in this study of nifH expression we only detected two phylotypes, and both were phylogenetically related to cyanobacterial nifH genes. One of the phylotypes was closely related to a nifH sequence from the filamentous, heterocystous cyanobacterium Anabaena cylindrica, and was found at the head of the estuary. The other phylotype was found in a sample collected near the mouth of the estuary and was closely related to nifH sequences from Group A unicellular cyanobacteria, which has previously been reported in oceanic waters only. These nifH phylotypes had distinct patterns of expression that were restricted to different regions of the Chesapeake Bay. This study provides the first evidence of nifH expression in the Chesapeake Bay, and suggests that diazotrophic unicellular cyanobacteria have a broader distribution and activity than previously recognized.
Collapse
Affiliation(s)
- Steven M Short
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA.
| | | |
Collapse
|