1
|
Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
Collapse
Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| |
Collapse
|
2
|
Electrochemical enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode of bioelectrochemical systems. iScience 2021; 24:102682. [PMID: 34195563 PMCID: PMC8233197 DOI: 10.1016/j.isci.2021.102682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/25/2021] [Accepted: 05/31/2021] [Indexed: 12/01/2022] Open
Abstract
Electrotrophic microorganisms have not been well studied in extreme environments. Here, we report on the nitrate-reducing cathodic microbial biofilm from a haloalkaline environment. The biofilm enriched via electrochemical approach under 9.5 pH and 20 g NaCl/L salinity conditions achieved −43.5±7.2μA/cm2 current density and 49.5±13.2%nitrate reduction efficiency via partial and complete denitrification. Voltammetric characterization of the biocathodes revealed a redox center with −0.294±0.003V (vs. Ag/AgCl) formal potential putatively involved in the electron uptake process. The lack of soluble redox mediators and hydrogen-driven nitrate reduction suggests direct-contact cathodic electron uptake by the nitrate-reducing microorganisms in the enriched biofilm. 16S-rRNA amplicon sequencing of the cathodic biofilm revealed the presence of unreported Pseudomonas, Natronococcus, and Pseudoalteromonas spp. at 31.45%,11.82%, and 9.69% relative sequence abundances, respectively. The enriched nitrate-reducing microorganisms also reduced nitrate efficiently using soluble electron donors found in the lake sediments, thereby suggesting their role in N-cycling in such environments. Enrichment of haloalkaliphilic nitrate-reducing microbial biofilm at the cathode Cathodic reduction current corresponded to the nitrate reduction process Pseudomonas, Natronococcus, and Pseudoalteromonas spp. enriched in the cathodic biofilm Enriched culture reduced nitrate efficiently with soluble electron donor sources
Collapse
|
3
|
Li S, Luo Z, Ji G. Seasonal function succession and biogeographic zonation of assimilatory and dissimilatory nitrate-reducing bacterioplankton. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1518-1525. [PMID: 29801245 DOI: 10.1016/j.scitotenv.2018.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
The dominance of different nitrate-reducing pathways determines nitrogen cycling patterns. Denitrification (DNF) has been widely studied, but assimilatory nitrate reduction (ANR) and dissimilatory nitrate reduction to ammonium (DNRA) have received much less attention. Their ecological patterns and responsible microbes are poorly understood. Here, we studied the structure and function succession of the three functional groups in the middle route of the South-to-North Water Diversion Project, which is a 1230 km canal spanning 8 degrees of latitude. The results reflected a nitrogen-removing pattern dominated by DNF in the summer and a nitrogen-retaining pattern dominated by ANR and DNRA in the winter. Stenotrophomonas, a typical denitrifier, was the keystone species in the summer and contributed to N2O production. Clostridium, a genus able to conduct ANR and DNRA, was the keystone species in the winter. Notably, a significant zonation pattern was discovered. According to the community structure, the system could be separated into two biogeographic zones, and the Yellow River (about latitude 35°N) is an important cut-off line. This bacterial biogeography followed different water characteristics and ecological processes. ANR was found to be an important process and seasonally transformed its habitat from the northern zone to the southern zone. DNRA bacteria were acclimated to the northern zone and favored at this region in both seasons. The generation of N2O, a strong greenhouse gas, also exhibited this zonation pattern. This is the first study to consider assimilatory and dissimilatory nitrate reducers together at a molecular level, and provides new insights into the underlying patterns of a nitrate-reducing bacterioplankton community.
Collapse
Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Zhongxin Luo
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|
4
|
Successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota from the Pearl River estuary to the northern South China Sea. Appl Microbiol Biotechnol 2018; 102:8035-8048. [PMID: 29946932 DOI: 10.1007/s00253-018-9147-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/05/2018] [Accepted: 05/23/2018] [Indexed: 01/09/2023]
Abstract
Thaumarchaeota and Bathyarchaeota (formerly named Miscellaneous Crenarchaeotal Group, MCG) are globally occurring archaea playing potential roles in nitrogen and carbon cycling, especially in marine benthic biogeochemical cycle. Information on their distributional and compositional patterns could provide critical clues to further delineate their physiological and biochemical characteristics. Profiles of thaumarchaeotal and the total archaeal community in the northern South China Sea surface sediments revealed a successively transitional pattern of Thaumarchaeota composition using MiSeq sequencing. Shallow-sea sediment enriched phylotypes decreased gradually along the slope from estuarine and coastal marine region to the deep-sea, while deep-sea sediment enriched phylotypes showed a trend of increasing. Proportion of Thaumarchaeota within the total archaea increased with seawater depth. Phylotypes enriched in shallow- and deep-sea sediments were affiliated to OTUs originated from similar niches, suggesting that physiological adaption not geographical distance shaped the distribution of Thaumarchaeota lineages. Quantitative PCR also depicted a successive decrease of thaumarchaeotal 16S rRNA gene abundance from the highest at shallow-sea sites E708S and E709S (2.57 × 106 and 2.73 × 106 gene copies/g of dry sediment) to the lowest at deep-sea sites E525S and E407S (1.97 × 106 and 2.14 × 106 gene copies/g of dry sediment). Both of the abundance fractions of Bathyarchaeota subgroups (including subgroups 1, 6, 8, 10, 13, 15, 17, and ungrouped Bathyarchaeota) and the total Bathyarchaeota in the total archaea showed a negative distribution to seawater depth. Partitioned distribution of Bathyarchaeota fraction in the total archaea is documented for the first time in this study, and the shallow- and deep-sea Bathyarchaeota could account for 17.8 and 0.8%, respectively, on average. Subgroups 6 and 8, enriched subgroups in shallow-sea sediments, largely explained this partitioned distribution pattern according to seawater depth. Their prevalence in shallow-sea and suboxic estuarine sediments rather than deep-sea sediments hints that their metabolic properties of carbon metabolism are adapted to carbon substrates in these environments.
Collapse
|
5
|
Zhang Y, Li J, Cheng X, Luo Y, Mai Z, Zhang S. Community differentiation of bacterioplankton in the epipelagic layer in the South China Sea. Ecol Evol 2018; 8:4932-4948. [PMID: 29876071 PMCID: PMC5980402 DOI: 10.1002/ece3.4064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/11/2018] [Accepted: 03/13/2018] [Indexed: 01/01/2023] Open
Abstract
The South China Sea (SCS) is the largest marginal sea in the western tropical Pacific Ocean and is characterized by complex physicochemical environments. To date, the biogeographic patterns of the microbial communities have rarely been reported at a basin scale in the SCS. In this study, the bacterial assemblages inhabiting the epipelagic zone across 110°E to 119°E along 14°N latitude were uncovered. The vertical stratification of both bacterial taxa and their potential functions were revealed. These results suggest that the water depth-specific environment is a driver of the vertical bacterioplankton distribution. Moreover, the bacterial communities were different between the eastern stations and the western stations, where the environmental conditions were distinct. However, the mesoscale eddy did not show an obvious effect on the bacterial community due to the large distance between the sampling site and the center of the eddy. In addition to the water depth and longitudinal location of the samples, the heterogeneity of the phosphate and salinity concentrations also significantly contributed to the variance in the epipelagic bacterial community in the SCS. To the best of our knowledge, this study is the first to report that the variability in epipelagic bacterioplankton is driven by the physicochemical environment at the basin scale in the SCS. Our results emphasize that the ecological significance of bacterioplankton can be better understood by considering the relationship between the biogeographic distribution of bacteria and the oceanic dynamics processes.
Collapse
Affiliation(s)
- Yi Zhang
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xuhua Cheng
- State Key Laboratory of Tropical OceanographySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Yinfeng Luo
- Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio‐resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| |
Collapse
|
6
|
Vilela Steiner L, Toledo Ramos D, Rubini Liedke AM, Serbent MP, Corseuil HX. Ethanol content in different gasohol blend spills influences the decision-making on remediation technologies. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 212:8-16. [PMID: 29427942 DOI: 10.1016/j.jenvman.2018.01.071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/16/2018] [Accepted: 01/26/2018] [Indexed: 06/08/2023]
Abstract
Gasohol blend spills with variable ethanol content exert different electron acceptor demands in groundwater and the distinct dynamics undergone by these blends underscores the need for field-based information to aid decision-making on suitable remediation technologies for each gasohol blend spill. In this study, a comparison of two gasohol releases (E10 (10:90 ethanol and gasoline, v/v) and E25 (25:75 ethanol and gasoline, v/v) under monitored natural attenuation (MNA) and nitrate biostimulation, respectively) was conducted to assess the most effective remediation strategy for each gasohol release. Microbial communities were assessed to support geochemical data as well as to enable the characterization of important population shifts that evolve during biodegradation processes in E25 and E10 field experiments. Results revealed that natural attenuation processes sufficiently supported ethanol and BTEX compounds biodegradation in E10 release, due to the lower biochemical oxygen demand they exert relative to E25 blend. In E25 release, nitrate reduction was largely responsible for BTEX and ethanol biodegradation, as intended. First-order decay constants demonstrated that ethanol degradation rates were similar (p < 0.05) for both remediation technologies (2.05 ± 0.15 and 2.22 ± 0.23, for E25 and E10, respectively) whilst BTEX compounds exhibited different degradation rates (p > 0.05) that were higher for the experiment under MNA (0.33 ± 0.06 and 0.43 ± 0.03, for E25 and E10, respectively). Therefore, ethanol content in different gasohol blends can influence the decision-making on the most suitable remediation technology, as MNA processes can be applied for the remediation of gasohol blends with lower ethanol content (i.e., 10% v/v), once the aquifer geochemical conditions provide a sufficient electron acceptor pool. To the best of our knowledge, this is the first field study to monitor two long-term gasohol releases over various time scales in order to assess feasible remediation technologies for each scenario.
Collapse
Affiliation(s)
- Leonardo Vilela Steiner
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil
| | - Débora Toledo Ramos
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil
| | - Ana Maria Rubini Liedke
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil
| | - Maria Pilar Serbent
- State University of Santa Catarina, Department of Sanitary Engineering, Ibirama, Santa Catarina, Brazil
| | - Henry Xavier Corseuil
- Federal University of Santa Catarina, Department of Sanitary and Environmental Engineering, Florianópolis, Santa Catarina, Brazil.
| |
Collapse
|
7
|
Morando M, Capone DG. Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP). Front Microbiol 2016; 7:1932. [PMID: 27994576 PMCID: PMC5133248 DOI: 10.3389/fmicb.2016.01932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/17/2016] [Indexed: 11/13/2022] Open
Abstract
Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, the roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake) with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP) to assess the ability of individual phylotypes to assimilate a specific N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II. Alternatively, this may suggest the existence of tightly coupled metabolisms with primary assimilators, e.g., symbiosis, or the rapid and efficient scavenging of recently released products by highly active individuals. These results may be connected with global dominance often seen with these clades, likely conferring an advantage over other clades unable to access these resources. We also provide new direct evidence of in situ nitrate utilization by the cyanobacterium Prochlorococcus in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e., different levels of nitrogen assimilation within clades, likely reflecting niche partitioning by ecotypes.
Collapse
Affiliation(s)
- Michael Morando
- Marine and Environmental Biology, University of Southern California Los Angeles, CA, USA
| | - Douglas G Capone
- Marine and Environmental Biology, University of Southern California Los Angeles, CA, USA
| |
Collapse
|
8
|
Jiang X, Jiao N. Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes. Indian J Microbiol 2016; 56:309-17. [PMID: 27407295 PMCID: PMC4920764 DOI: 10.1007/s12088-016-0585-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 04/12/2016] [Indexed: 11/25/2022] Open
Abstract
Bacteria play an important role in the marine biogeochemical cycles. However, research on the bacterial community structure of the Indian Ocean is scarce, particularly within the vertical dimension. In this study, we investigated the bacterial diversity of the pelagic, mesopelagic and bathypelagic zones of the southwestern Indian Ocean (50.46°E, 37.71°S). The clone libraries constructed by 16S rRNA gene sequence revealed that most phylotypes retrieved from the Indian Ocean were highly divergent from those retrieved from other oceans. Vertical differences were observed based on the analysis of natural bacterial community populations derived from the 16S rRNA gene sequences. Based on the analysis of the nasA gene sequences from GenBank database, a pair of general primers was developed and used to amplify the bacterial nitrate-assimilating populations. Environmental factors play an important role in mediating the bacterial communities in the Indian Ocean revealed by canonical correlation analysis.
Collapse
Affiliation(s)
- Xuexia Jiang
- />Editorial Office of Journal of Zhaoqing University, 526061 Guangdong, China
| | - Nianzhi Jiao
- />State Key Laboratory of Marine Environmental Science, Xiamen University, 361102 Xiamen, China
| |
Collapse
|
9
|
Jiang X, Dang H, Jiao N. Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments. PLoS One 2015; 10:e0117473. [PMID: 25647610 PMCID: PMC4315400 DOI: 10.1371/journal.pone.0117473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/25/2014] [Indexed: 12/15/2022] Open
Abstract
Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.
Collapse
Affiliation(s)
- Xuexia Jiang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen 361102, China
| |
Collapse
|
10
|
Brauer VS, Stomp M, Bouvier T, Fouilland E, Leboulanger C, Confurius-Guns V, Weissing FJ, Stal L, Huisman J. Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community. Front Microbiol 2015; 5:795. [PMID: 25642224 PMCID: PMC4294207 DOI: 10.3389/fmicb.2014.00795] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 12/23/2014] [Indexed: 11/13/2022] Open
Abstract
N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece sp. Miami BG043511 and its associated free-living chemotrophic bacteria at different concentrations of nitrate and dissolved organic carbon and different temperatures. High temperature strongly stimulated the growth of Cyanothece, but had less effect on the growth and community composition of the chemotrophic bacteria. Conversely, nitrate and carbon addition did not significantly increase the abundance of Cyanothece, but strongly affected the abundance and species composition of the associated chemotrophic bacteria. In nitrate-free medium the associated bacterial community was co-dominated by the putative diazotroph Mesorhizobium and the putative aerobic anoxygenic phototroph Erythrobacter and after addition of organic carbon also by the Flavobacterium Muricauda. Addition of nitrate shifted the composition toward co-dominance by Erythrobacter and the Gammaproteobacterium Marinobacter. Our results indicate that Cyanothece modified the species composition of its associated bacteria through a combination of competition and facilitation. Furthermore, within the bacterial community, niche differentiation appeared to play an important role, contributing to the coexistence of a variety of different functional groups. An important implication of these findings is that changes in nitrogen and carbon availability due to, e.g., eutrophication and climate change are likely to have a major impact on the species composition of the bacterial community associated with N2-fixing cyanobacteria.
Collapse
Affiliation(s)
- Verena S. Brauer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
- Department of Theoretical Biology, Center for Ecological and Evolutionary Studies, University of GroningenGroningen, Netherlands
- Laboratoire Ecologie des Systèmes Marins Côtiers ECOSYM, UMR 5119, CNRS, IRD, Ifremer, Université Montpellier 2Montpellier, France
| | - Maayke Stomp
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Thierry Bouvier
- Laboratoire Ecologie des Systèmes Marins Côtiers ECOSYM, UMR 5119, CNRS, IRD, Ifremer, Université Montpellier 2Montpellier, France
| | - Eric Fouilland
- Laboratoire Ecologie des Systèmes Marins Côtiers ECOSYM, UMR 5119, CNRS, IRD, Ifremer, Université Montpellier 2Montpellier, France
| | - Christophe Leboulanger
- Laboratoire Ecologie des Systèmes Marins Côtiers ECOSYM, UMR 5119, CNRS, IRD, Ifremer, Université Montpellier 2Montpellier, France
| | - Veronique Confurius-Guns
- Department of Marine Microbiology, Royal Netherlands Institute for Sea ResearchYerseke, Netherlands
| | - Franz J. Weissing
- Department of Theoretical Biology, Center for Ecological and Evolutionary Studies, University of GroningenGroningen, Netherlands
| | - LucasJ. Stal
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
- Department of Marine Microbiology, Royal Netherlands Institute for Sea ResearchYerseke, Netherlands
| | - Jef Huisman
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| |
Collapse
|
11
|
Li J, Li N, Li F, Zou T, Yu S, Wang Y, Qin S, Wang G. Spatial diversity of bacterioplankton communities in surface water of northern South China Sea. PLoS One 2014; 9:e113014. [PMID: 25402458 PMCID: PMC4234503 DOI: 10.1371/journal.pone.0113014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 10/21/2014] [Indexed: 11/23/2022] Open
Abstract
The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.
Collapse
Affiliation(s)
- Jialin Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Nan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Fuchao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tao Zou
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Shuxian Yu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Yinchu Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- * E-mail: (SQ); (GW)
| | - Guangyi Wang
- Tianjin University Center for Marine Environmental Ecology, School of Environmental Sciences and Engineering, Tianjin University, Tianjin, China
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail: (SQ); (GW)
| |
Collapse
|
12
|
Li M, Hong Y, Cao H, Gu JD. Community structures and distribution of anaerobic ammonium oxidizing and nirS-encoding nitrite-reducing bacteria in surface sediments of the South China Sea. MICROBIAL ECOLOGY 2013; 66:281-296. [PMID: 23354291 DOI: 10.1007/s00248-012-0175-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/26/2012] [Indexed: 06/01/2023]
Abstract
Anaerobic ammonium oxidation (anammox) and denitrification are two important processes responsible for nitrogen loss; monitoring of microbial communities carrying out these two processes offers a unique opportunity to understand the microbial nitrogen cycle. The aim of the current study was to characterize community structures and distribution of anammox and nirS-encoding nitrite-reducing bacteria in surface sediments of the northern South China Sea (SCS). The consistent phylogenetic results of three biomarkers of anammox bacteria, including 16S rRNA, hzo, and Scalindua-nirS genes, showed that Scalindua-like bacteria were the only anammox group presenting in surface sediments of the SCS. However, a relatively high micro-diversity was found within this group, including several SCS habitat-specific phylotypes, Candidatus "Scalindua zhenghei". Comparing to 16S rRNA gene, hzo and Scalindua-nirS genes provided a relatively higher resolution to elucidate anammox bacteria. For the nirS-encoding nitrite-reducing bacteria, the detected nirS gene sequences were closely related to various marine nirS denitrifiers, especially those which originated from coastal and estuarine sediments with a much higher diversity than anammox bacteria. Anammox bacterial communities shifted along with the seawater depth, while nirS-encoding nitrite-reducing bacteria did not. Although nirS-encoding nitrite-reducing bacteria have a much higher abundance and diversity than anammox bacteria, they showed similar abundance variation patterns in research sites, suggesting the two microbial groups might be affected by the similar environmental factors. The significant correlations among the abundance of the two microbial groups with the molar ratio of NH4 (+) to (NO2 (-) + NO3 (-)), pH, and organic matters of sediments strongly supported this hypothesis.
Collapse
Affiliation(s)
- Meng Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | | | | | | |
Collapse
|
13
|
Li Z, Jin W, Liang Z, Yue Y, Lv J. Abundance and diversity of ammonia-oxidizing archaea in response to various habitats in Pearl River Delta of China, a subtropical maritime zone. J Environ Sci (China) 2013; 25:1195-1205. [PMID: 24191610 DOI: 10.1016/s1001-0742(12)60178-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments. However, little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district. To understand the abundance, diversity, and distribution of AOA in Pearl River Delta of China in response to various habitats, the archaeal amoA genes in soil, marine, river, lake, hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries. Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades, i.e., estuary sediment, marine water/sediment, soil, hot spring and Cluster 1. Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation. The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature, pH, total organic carbon, total nitrogen and dissolved oxygen variables. Assessing AOA amoA gene copy numbers, ranging from 6.84 x 10(6) to 9.45 x 10(7) copies/g in dry soil/sediment, and 6.06 x 10(6) to 2.41 x 10(7) copies/L in water samples, were higher than ammonia-oxidizing bacteria (AOB) by 1-2 orders of magnitude. However, AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples. Overall, these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge. The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters. New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.
Collapse
Affiliation(s)
- Zhixin Li
- Shenzhen Key Laboratory of Water Resource Utilization and Environmental Pollution Control, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China.
| | | | | | | | | |
Collapse
|
14
|
Wang W, Ji X, Yuan C, Dai F, Zhu J, Sun M. A method for molecular analysis of catalase gene diversity in seawater. Indian J Microbiol 2013; 53:477-81. [PMID: 24426153 DOI: 10.1007/s12088-013-0404-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 02/28/2013] [Indexed: 11/30/2022] Open
Abstract
Catalase plays an important role in the metabolism of marine bacteria and has potential impact on the marine environment. Four PCR primers were designed to amplify the catalase gene fragments in marine bacteria by applying metagenomic DNA from Yellow Sea surface water as the template. Of the four reproducible target PCR products, the longest one with 900 bp were chosen for catalase gene library construction by the T-vector and the white Escherichia coli colonies in the library was screened through restriction-digesting the reamplified insert fragments by the selected restriction endonuclease MboI, and then the bands of the resulting products were displayed in the agarose gel by electrophoresis. The unique restriction fragment length polymorphism (RFLP) pattern was selected and the corresponding catalase gene fragments were sequenced, which verified that every unique RFLP pattern represented one type of catalase. This PCR-RFLP method above was established to investigate the bacterial catalase diversity in seawater.
Collapse
Affiliation(s)
- Wei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071 China
| | - Xiaofeng Ji
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071 China
| | - Cui Yuan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071 China
| | - Fangqun Dai
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071 China
| | - Jiancheng Zhu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071 China
| | - Mi Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071 China ; Marine Products Resource and Enzyme Engineering Laboratory, Yellow Sea Fisheries Research Institute, 106 Nanjing Road, Qingdao, 266071 Shandong China
| |
Collapse
|
15
|
Wawrik B, Boling WB, Van Nostrand JD, Xie J, Zhou J, Bronk DA. Assimilatory nitrate utilization by bacteria on the West Florida Shelf as determined by stable isotope probing and functional microarray analysis. FEMS Microbiol Ecol 2011; 79:400-11. [PMID: 22092701 DOI: 10.1111/j.1574-6941.2011.01226.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/04/2011] [Accepted: 10/07/2011] [Indexed: 11/29/2022] Open
Abstract
Dissolved inorganic nitrogen (DIN) uptake by marine heterotrophic bacteria has important implications for the global nitrogen (N) and carbon (C) cycles. Bacterial nitrate utilization is more prevalent in the marine environment than traditionally thought, but the taxonomic identity of bacteria that utilize nitrate is difficult to determine using traditional methodologies. (15) N-based DNA stable isotope probing was applied to document direct use of nitrate by heterotrophic bacteria on the West Florida Shelf. Seawater was incubated in the presence of 2 μM (15) N ammonium or (15) N nitrate. DNA was extracted, fractionated via CsCl ultracentrifugation, and each fraction was analyzed by terminal restriction fragment length polymorphism (TRFLP) analysis. TRFs that exhibited density shifts when compared to controls that had not received (15) N amendments were identified by comparison with 16S rRNA gene sequence libraries. Relevant marine proteobacterial lineages, notably Thalassobacter and Alteromonadales, displayed evidence of (15) N incorporation. RT-PCR and functional gene microarray analysis could not demonstrate the expression of the assimilatory nitrate reductase gene, nasA, but mRNA for dissimilatory pathways, i.e. nirS, nirK, narG, nosZ, napA, and nrfA was detected. These data directly implicate several bacterial populations in nitrate uptake, but suggest a more complex pattern for N flow than traditionally implied.
Collapse
Affiliation(s)
- Boris Wawrik
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
| | | | | | | | | | | |
Collapse
|
16
|
Cao H, Hong Y, Li M, Gu JD. Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea. Antonie van Leeuwenhoek 2011; 100:545-56. [PMID: 21717206 PMCID: PMC3190089 DOI: 10.1007/s10482-011-9610-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/10/2011] [Indexed: 11/26/2022]
Abstract
In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious community structure shift for both AOA and beta-AOB from the coastal marginal areas to the slope in the deep-sea was detected, while the OTU numbers of AOA amoA were more stable than those of the beta-AOB. The OTUs of beta-AOB increased with the distance from the coastal margin areas to the slope in the deep-sea. Beta-AOB showed lower diversity with dominant strains in a polluted area but higher diversity without dominant strains in a clean area. Moreover, the diversity of beta-AOB was correlated with pH values, while no noticeable relationships were established between AOA and physicochemical parameters. Beta-AOB was more sensitive to transect environmental variability and might be a potential indicator for environmental changes. Additionally, the surface sediments surveyed in the South China Sea harboured diverse and distinct AOA and beta-AOB phylotypes different from other environments, suggesting the endemicity of some nitrifying prokaryotes in the South China Sea.
Collapse
Affiliation(s)
- Huiluo Cao
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | | | | | | |
Collapse
|
17
|
Zehr JP, Kudela RM. Nitrogen cycle of the open ocean: from genes to ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:197-225. [PMID: 21329204 DOI: 10.1146/annurev-marine-120709-142819] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The marine nitrogen (N) cycle controls the productivity of the oceans. This cycle is driven by complex biogeochemical transformations, including nitrogen fixation, denitrification, and assimilation and anaerobic ammonia oxidation, mediated by microorganisms. New processes and organisms continue to be discovered, complicating the already complex picture of oceanic N cycling. Genomics research has uncovered the diversity of nitrogen metabolism strategies in phytoplankton and bacterioplankton. The elemental ratios of nutrients in biological material are more flexible than previously believed, with implications for vertical export of carbon and associated nutrients to the deep ocean. Estimates of nitrogen fixation and denitrification continue to be modified, and anaerobic ammonia oxidation has been identified as a new process involved in denitrification in oxygen minimum zones. The nitrogen cycle in the oceans is an integral feature of the function of ocean ecosystems and will be a central player in how oceans respond during global environmental change.
Collapse
Affiliation(s)
- Jonathan P Zehr
- Ocean Sciences Department, University of California, Santa Cruz, California 95064, USA.
| | | |
Collapse
|
18
|
Increasing the microbial carbon sink in the sea by reducing chemical fertilization on the land. Nat Rev Microbiol 2010. [DOI: 10.1038/nrmicro2386-c2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|