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Wang H, Liu F, Wang M, Bettarel Y, Eissler Y, Chen F, Kan J. Planktonic eukaryotes in the Chesapeake Bay: contrasting responses of abundant and rare taxa to estuarine gradients. Microbiol Spectr 2024; 12:e0404823. [PMID: 38606959 PMCID: PMC11064499 DOI: 10.1128/spectrum.04048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
Phytoplankton are important drivers of aquatic ecosystem function and environmental health. Their community compositions and distributions are directly impacted by environmental processes and human activities, including in the largest estuary in North America, the Chesapeake Bay. It is crucial to uncover how planktonic eukaryotes play fundamental roles as primary producers and trophic links and sustain estuarine ecosystems. In this study, we investigated the detailed community structure and spatiotemporal variations of planktonic eukaryotes in the Chesapeake Bay across space and time for three consecutive years. A clear seasonal and spatial shift of total, abundant, and rare planktonic eukaryotes was evident, and the pattern recurred interannually. Multiple harmful algal species have been identified in the Bay with varied distribution patterns, such as Karlodinium, Heterosigma akashiwo, Protoperidinium sp., etc. Compared to abundant taxa, rare subcommunities were more sensitive to environmental disturbance in terms of richness, diversity, and distribution. The combined effects of temporal variation (13.3%), nutrient availability (10.0%), and spatial gradients (8.8%) structured the distribution of eukaryotic microbial communities in the Bay. Similar spatiotemporal patterns between planktonic prokaryotes and eukaryotes suggest common mechanisms of adjustment, replacement, and species interaction for planktonic microbiomes under strong estuarine gradients. To our best knowledge, this work represents the first systematic study on planktonic eukaryotes in the Bay. A comprehensive view of the distribution of planktonic microbiomes and their interactions with environmental processes is critical in understanding the underlying microbial mechanisms involved in maintaining the stability, function, and environmental health of estuarine ecosystems. IMPORTANCE Deep sequencing analysis of planktonic eukaryotes in the Chesapeake Bay reveals high community diversity with many newly recognized phytoplankton taxa. The Chesapeake Bay planktonic eukaryotes show distinct seasonal and spatial variability, with recurring annual patterns of total, abundant, and rare groups. Rare taxa mainly contribute to eukaryotic diversity compared to abundant groups, and they are more sensitive to spatiotemporal variations and environmental filtering. Temporal variations, nutrient availability, and spatial gradients significantly affect the distribution of eukaryotic microbial communities. Similar spatiotemporal patterns in prokaryotes and eukaryotes suggest common mechanisms of adjustment, substitution, and species interactions in planktonic microbiomes under strong estuarine gradients. Interannually recurring patterns demonstrate that diverse eukaryotic taxa have well adapted to the estuarine environment with a long residence time. Further investigations of how human activities impact estuarine planktonic eukaryotes are critical in understanding their essential ecosystem roles and in maintaining environmental safety and public health.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Feilong Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, China
| | - Yvan Bettarel
- ECOSYM (Ecologie des systèmes marins côtiers)- UMR 5119, Universite de Montpellier, Montpellier, France
| | - Yoanna Eissler
- Laboratorio de Virología, Centro de Neurobiología y Fisiopatología Integrativa, Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, Arizona, USA
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Ding L, Chen H, Wang M, Wang P. Shrub expansion raises both aboveground and underground multifunctionality on a subtropical plateau grassland: coupling multitrophic community assembly to multifunctionality and functional trade-off. Front Microbiol 2024; 14:1339125. [PMID: 38274762 PMCID: PMC10808678 DOI: 10.3389/fmicb.2023.1339125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Shrubs have expanded into grasslands globally. However, the relative importance of aboveground and underground diversity and the relative importance of underground community assembly and diversity in shaping multifunctionality and functional trade-offs over shrub expansion remains unknown. Methods In this study, aboveground and underground multitrophic communities (abundant and rare archaea, bacteria, fungi, nematodes, and protists) and 208 aboveground and underground ecosystem properties or indicators were measured at three stages (Grass, Mosaic, Shrub) of shrub expansion on the Guizhou subtropical plateau grassland to study multifunctionality and functional trade-offs. Results The results showed that shrub expansion significantly enhanced aboveground, underground, and entire ecosystem multifunctionality. The functional trade-off intensities of the aboveground, underground, and entire ecosystems showed significant V-shaped changes with shrub expansion. Shrub expansion improved plant species richness and changed the assembly process and species richness of soil abundant and rare subcommunities. Plant species diversity had a greater impact on multifunctionality than soil microbial diversity by more than 16%. The effect of plant species diversity on functional trade-offs was only one-fifth of the effect of soil microbial diversity. The soil microbial species richness did not affect multifunctionality, however, the assembly process of soil microbial communities did. Rather than the assembly process of soil microbial communities, the soil microbial species richness affected functional trade-offs. Discussion Our study is the first to couple multitrophic community assemblies to multifunctionality and functional trade-offs. Our results would boost the understanding of the role of aboveground and underground diversity in multifunctionality and functional trade-offs.
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Affiliation(s)
- Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Hong Chen
- Guizhou Songbaishan Reservoir Management Office, Guiyang, Guizhou, China
| | - Mengya Wang
- College of Animal Science, Guizhou University, Guiyang, Guizhou, China
| | - Puchang Wang
- School of Life Science, Guizhou Normal University, Guiyang, Guizhou, China
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Zhong S, Hou B, Zhang J, Wang Y, Xu X, Li B, Ni J. Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater. Front Microbiol 2023; 14:1111383. [PMID: 37560528 PMCID: PMC10407230 DOI: 10.3389/fmicb.2023.1111383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.
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Affiliation(s)
- Sining Zhong
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bowen Hou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Jinzheng Zhang
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yichu Wang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bin Li
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
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He J, Tan X, Nie Y, Ma L, Liu J, Lu X, Mo J, Leloup J, Nunan N, Ye Q, Shen W. Distinct Responses of Abundant and Rare Soil Bacteria to Nitrogen Addition in Tropical Forest Soils. Microbiol Spectr 2023; 11:e0300322. [PMID: 36622236 DOI: 10.1128/spectrum.03003-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Soil microbial responses to anthropogenic nitrogen (N) enrichment at the overall community level has been extensively studied. However, the responses of community dynamics and assembly processes of the abundant versus rare bacterial taxa to N enrichment have rarely been assessed. Here, we present a study in which the effects of short- (2 years) and long-term (13 years) N additions to two nearby tropical forest sites on abundant and rare soil bacterial community composition and assembly were documented. The N addition, particularly in the long-term experiment, significantly decreased the bacterial α-diversity and shifted the community composition toward copiotrophic and N-sensitive species. The α-diversity and community composition of the rare taxa were more affected, and they were more closely clustered phylogenetically under N addition compared to the abundant taxa, suggesting the community assembly of the rare taxa was more governed by deterministic processes (e.g., environmental filtering). In contrast, the abundant taxa exhibited higher community abundance, broader environmental thresholds, and stronger phylogenetic signals under environmental changes than the rare taxa. Overall, these findings illustrate that the abundant and rare bacterial taxa respond distinctly to N addition in tropical forests, with higher sensitivity of the rare taxa, but potentially broader environmental acclimation of the abundant taxa. IMPORTANCE Atmospheric nitrogen (N) deposition is a worldwide environmental problem and threatens biodiversity and ecosystem functioning. Understanding the responses of community dynamics and assembly processes of abundant and rare soil bacterial taxa to anthropogenic N enrichment is vital for the management of N-polluted forest soils. Our sequence-based data revealed distinct responses in bacterial diversity, community composition, environmental acclimation, and assembly processes between abundant and rare taxa under N-addition soils in tropical forests. These findings provide new insight into the formation and maintenance of bacterial diversity and offer a way to better predict bacterial responses to the ongoing atmospheric N deposition in tropical forests.
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Ren Z, Zhang C, Li X, Ma K, Cui B. Abundant and Rare Bacterial Taxa Structuring Differently in Sediment and Water in Thermokarst Lakes in the Yellow River Source Area, Qinghai-Tibet Plateau. Front Microbiol 2022; 13:774514. [PMID: 35422785 PMCID: PMC9002311 DOI: 10.3389/fmicb.2022.774514] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/02/2022] [Indexed: 01/28/2023] Open
Abstract
Thermokarst lakes are forming from permafrost thaw and are severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remains largely unknown, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided into abundant and rare according to their relative abundance, and the Sorensen dissimilarity (βsor) was partitioned into turnover (βturn) and nestedness (βnest). The whole bacterial communities and the abundant and rare subcommunities differed substantially between sediment and water in taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. In general, bacterial communities are predominantly governed by strong turnover processes (βturn/βsor ratio of 0.925). Bacterial communities in sediment had a significantly higher βturn/βsor ratio than in water. Abundant subcommunities were significantly lower in the βturn/βsor ratio compared with rare subcommunities. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by heterogeneity in the source material, environmental filtering, and geographical isolation, leading to compositionally distinct communities. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapidly changing and vulnerable ecosystems.
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Affiliation(s)
- Ze Ren
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Environment, Beijing Normal University, Beijing, China
| | - Cheng Zhang
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Engineering Technology, Beijing Normal University, Zhuhai, China
| | - Xia Li
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Environment, Beijing Normal University, Beijing, China
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China.,School of Environment, Beijing Normal University, Beijing, China
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Shao Q, Sun D, Fang C, Feng Y, Wang C. Biodiversity and Biogeography of Abundant and Rare Microbial Assemblages in the Western Subtropical Pacific Ocean. Front Microbiol 2022; 13:839562. [PMID: 35432250 PMCID: PMC9006148 DOI: 10.3389/fmicb.2022.839562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The levels of chlorophyll a and nutrient concentrations in the surface waters of the western subtropical Pacific Ocean are among the lowest globally. In addition, our knowledge of basin-scale diversity and biogeography of microbial communities in this vast extremely oligotrophic environment is still rather limited. Here, high-throughput sequencing was used to examine the biodiversity and biogeography of abundant and rare microbial assemblages throughout the water column from the surface to a depth of 3,000 m across a horizontal distance of 1,100 km in the western Pacific Ocean. Microbial alpha diversity in the 200-m layer was higher than at other depths, with Gammaproteobacteria, Alphaproteobacteria, and Clostridia as the dominant classes in all samples. Distinctly vertical distributions within the microbial communities were revealed, with no difference horizontally. Some microbes exhibited depth stratification. For example, the relative abundances of Cyanobacteria and Alphaproteobacteria decreased with depth, while Nitrososphaeria, Actinobacteria, and Gammaproteobacteria increased with depth in the aphotic layers. Furthermore, we found that environmental (selective process) and spatial (neutral process) factors had different effects on abundant and rare taxa. Geographical distance showed little effect on the dispersal of all and abundant taxa, while statistically significant distance-decay relationships were observed among the rare taxa. Temperature and chlorophyll a were strongly associated with all, abundant, and rare taxa in the photic layers, while total inorganic nitrogen was recognized as the crucial factor in the aphotic layers. Variance partitioning analysis indicated that environmental selection played a relatively important role in shaping all and abundant taxa, while the variation in rare taxa explained by environmental and spatial processes was relatively low, as more than 70% of the variation remained unexplained. This study provides novel knowledge related to microbial community diversity in the western subtropical Pacific Ocean, and the analyzes biogeographical patterns among abundant and rare taxa.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Ningbo Institute of Oceanography, Ningbo, China
| | - Dong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chen Fang
- College of Oceanography, Hohai University, Nanjing, China
| | - Yunzhi Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Dong Y, Wu S, Deng Y, Wang S, Fan H, Li X, Bai Z, Zhuang X. Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses. Front Microbiol 2021; 12:689762. [PMID: 34276621 PMCID: PMC8283415 DOI: 10.3389/fmicb.2021.689762] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromatic hydrocarbon (PAH) stress alters the stability and functions of the abundant and rare taxa. Here, we performed soil microcosms with gradient pyrene stresses as a model ecosystem to explore the roles of community assembly in determining structures and functions of the abundant and rare subcommunities. The dose–effect of pyrene significantly altered compositions of abundant and rare subcommunities. With increasing pyrene stresses, diversity increased in abundant subcommunities, while it decreased in the rare. Importantly, the abundant taxa exhibited a much broader niche width and environmental adaptivity than the rare, contributing more to pyrene biodegradation, whereas rare taxa played a key role in improving subcommunity resistance to stress, potentially promoting community persistence and stability. Furthermore, subcommunity co-occurrence network analysis revealed that abundant taxa inclined to occupy the core and central position in adaptation to the pyrene stresses. Stochastic processes played key roles in the abundant subcommunity rather than the rare subcommunity. Overall, these findings extend our understanding of the ecological mechanisms and interactions of abundant and rare taxa in response to pollution stress, laying a leading theoretical basis that abundant taxa are core targets for biostimulation in soil remediation.
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Affiliation(s)
- Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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