1
|
Wang J, Guo X, Li Y, Song G, Zhao L. Understanding the Variation of Bacteria in Response to Summertime Oxygen Depletion in Water Column of Bohai Sea. Front Microbiol 2022; 13:890973. [PMID: 35756048 PMCID: PMC9221365 DOI: 10.3389/fmicb.2022.890973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Aiming to reveal the variation in bacteria community under oxygen depletion formed every summer in water column of central Bohai Sea, a time-scenario sampling from June to August in 2018 at a 20-day interval along one inshore-offshore transect was settled. Water samples were collected at the surface, middle, and bottom layer and then analyzed by high-throughput sequencing targeting both 16S rRNA and nosZ genes. Compared to the surface and middle water, oxygen depletion occurred at bottom layer in August. In top two layers, Cyanobacteria dominated the bacterial community, whereas heterotrophic bacteria became dominant in bottom water of Bohai Sea. Based on the time scenario, distinct community separation was observed before (June and July) and after (August) oxygen depletion (p = 0.003). Vertically, strict stratification of nosZ gene was stably formed along 3 sampling layers. As a response to oxygen depletion, the diversity indices of both total bacteria (16S rRNA) and nosZ gene-encoded denitrification bacteria all increased, which indicated the intense potential of nitrogen lose when oxygen depleted. Dissolved oxygen (DO) was the key impacting factor on the community composition of total bacteria in June, whereas nutrients together with DO play the important roles in August for both total and denitrifying bacteria. The biotic impact was revealed further by strong correlations which showed between Cyanobacteria and heterotrophic bacteria in June from co-occurrence network analysis, which became weak in August when DO was depleted. This study discovered the variation in bacteria community in oxygen-depleted water with further effort to understand the potential role of denitrifying bacteria under oxygen depletion in Bohai Sea for the first time, which provided insights into the microbial response to the world-wide expanding oxygen depletion and their contributions in the ocean nitrogen cycling.
Collapse
Affiliation(s)
- Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Xiaoxiao Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Yanying Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Guisheng Song
- School of Marine Science and Technology, Tianjin University, Tianjin, China
| | - Liang Zhao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
| |
Collapse
|
2
|
Zhang CJ, Chen YL, Sun YH, Pan J, Cai MW, Li M. Diversity, metabolism and cultivation of archaea in mangrove ecosystems. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:252-262. [PMID: 37073347 PMCID: PMC10077227 DOI: 10.1007/s42995-020-00081-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/19/2020] [Indexed: 05/03/2023]
Abstract
Mangroves comprise a globally significant intertidal ecosystem that contains a high diversity of microorganisms, including fungi, bacteria and archaea. Archaea is a major domain of life that plays important roles in biogeochemical cycles in these ecosystems. In this review, the potential roles of archaea in mangroves are briefly highlighted. Then, the diversity and metabolism of archaeal community of mangrove ecosystems across the world are summarized and Bathyarchaeota, Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Lokiarchaeota are confirmed as the most abundant and ubiquitous archaeal groups. The metabolic potential of these archaeal groups indicates their important ecological function in carbon, nitrogen and sulfur cycling. Finally, some cultivation strategies that could be applied to uncultivated archaeal lineages from mangrove wetlands are suggested, including refinements to traditional cultivation methods based on genomic and transcriptomic information, and numerous innovative cultivation techniques such as single-cell isolation and high-throughput culturing (HTC). These cultivation strategies provide more opportunities to obtain previously uncultured archaea.
Collapse
Affiliation(s)
- Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yu-Lian Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Yi-Hua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Ming-Wei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| |
Collapse
|
3
|
Laurent A, Fennel K. Time-Evolving, Spatially Explicit Forecasts of the Northern Gulf of Mexico Hypoxic Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14449-14458. [PMID: 31738049 DOI: 10.1021/acs.est.9b05790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Mississippi-Atchafalaya River Basin delivers large amounts of freshwater and nutrients to the northern Gulf of Mexico promoting the development of a large hypoxic zone every summer. Statistical and semiempirical models have long been used to provide seasonal forecasts of the mid-summer hypoxic extent using historic time series of spring nutrient load and mid-summer hypoxic extent. These forecasts consist of a scalar estimate of the hypoxic area with uncertainty but do not include spatial distributions or temporal evolution of hypoxic conditions. Three-dimensional (3D) circulation-biogeochemical models of the coastal ocean simulate the temporal evolution of hypoxia in a spatially explicit manner but have not yet been used for seasonal hypoxia forecasting. Here, we present a hybrid method for seasonal, spatially explicit, time-evolving forecasts of the hypoxic zone that combines statistical forecasting with information from a 3D biogeochemical model. The hybrid method uses spring nitrate load and a multiyear (1985-2018) 3D hindcast simulation to produce a seasonal forecast. Validation shows that the method explains up to 76% of the observed year-to-year variability in the hypoxic area. The forecasts suggest that the maximum seasonal extent of hypoxia is reached, on average, on August 13, 2 weeks after the completion of the annual cruise. An analysis of month-to-month variations in hypoxia forecasts due to variability in wind speed and freshwater discharge allows estimates of weather-related uncertainties in the forecast.
Collapse
Affiliation(s)
- Arnaud Laurent
- Department of Oceanography , Dalhousie University , Halifax B3H 4R2 , Nova Scotia , Canada
| | - Katja Fennel
- Department of Oceanography , Dalhousie University , Halifax B3H 4R2 , Nova Scotia , Canada
| |
Collapse
|
4
|
Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev 2018; 42:639-655. [PMID: 29790926 DOI: 10.1093/femsre/fuy023] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.
Collapse
Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.,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
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ji-Dong Gu
- 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
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| |
Collapse
|
5
|
Ortmann AC, Brannock PM, Wang L, Halanych KM. River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico. MICROBIAL ECOLOGY 2018; 76:941-953. [PMID: 29666882 DOI: 10.1007/s00248-018-1184-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.
Collapse
Affiliation(s)
- Alice C Ortmann
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA.
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, B2Y 4A2, Canada.
| | - Pamela M Brannock
- Department of Biological Science, Auburn University, Auburn, AL, 36849, USA
- Department of Biology, Rollins College, Winter Park, FL, 32789, USA
| | - Lei Wang
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA
| | - Kenneth M Halanych
- Department of Biological Science, Auburn University, Auburn, AL, 36849, USA
| |
Collapse
|
6
|
Mori F, Umezawa Y, Kondo R, Wada M. Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan). FEMS Microbiol Ecol 2018; 94:4951600. [DOI: 10.1093/femsec/fiy053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui 917-0003, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
| |
Collapse
|
7
|
Kaestli M, Skillington A, Kennedy K, Majid M, Williams D, McGuinness K, Munksgaard N, Gibb K. Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization. Front Microbiol 2017; 8:1313. [PMID: 28751882 PMCID: PMC5507994 DOI: 10.3389/fmicb.2017.01313] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 12/02/2022] Open
Abstract
Darwin Harbour in northern Australia is an estuary in the wet-dry tropics subject to increasing urbanization with localized water quality degradation due to increased nutrient loads from urban runoff and treated sewage effluent. Tropical estuaries are poorly studied compared to temperate systems and little is known about the microbial community-level response to nutrients. We aimed to examine the spatial and temporal patterns of the bacterial community and its association with abiotic factors. Since Darwin Harbour is macrotidal with strong seasonal patterns and mixing, we sought to determine if a human impact signal was discernible in the microbiota despite the strong hydrodynamic forces. Adopting a single impact–double reference design, we investigated the bacterial community using next-generation sequencing of the 16S rRNA gene from water and sediment from reference creeks and creeks affected by effluent and urban runoff. Samples were collected over two years during neap and spring tides, in the dry and wet seasons. Temporal drivers, namely seasons and tides had the strongest relationship to the water microbiota, reflecting the macrotidal nature of the estuary and its location in the wet-dry tropics. The neap-tide water microbiota provided the clearest spatial resolution while the sediment microbiota reflected current and past water conditions. Differences in patterns of the microbiota between different parts of the harbor reflected the harbor's complex hydrodynamics and bathymetry. Despite these variations, a microbial signature was discernible relating to specific effluent sources and urban runoff, and the composite of nutrient levels accounted for the major part of the explained variation in the microbiota followed by salinity. Our results confirm an overall good water quality but they also reflect the extent of some hypereutrophic areas. Our results show that the microbiota is a sensitive indicator to assess ecosystem health even in this dynamic and complex ecosystem.
Collapse
Affiliation(s)
- Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | - Anna Skillington
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | | | - Matthew Majid
- Aquatic Health Unit, Department of Environment and Natural Resources, Northern Territory GovernmentDarwin, NT, Australia
| | - David Williams
- Australian Institute of Marine ScienceDarwin, NT, Australia
| | - Keith McGuinness
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | - Niels Munksgaard
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwin, NT, Australia
| |
Collapse
|