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Shi Y, Li W, Guo X. Exploring environment-specific regulation: Characterizing bacterioplankton community dynamics in a typical lake of Inner Mongolia, China. ENVIRONMENTAL RESEARCH 2024; 253:119154. [PMID: 38754616 DOI: 10.1016/j.envres.2024.119154] [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: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Lakes serve as heterogeneous ecosystems with rich microbiota. Although previous studies on bacterioplankton have advanced our understanding, there are gaps in our knowledge concerning variations in the taxonomic composition and community assembly processes of bacterioplankton across different environment conditions. This study explored the spatial dynamics, assembly processes, and co-occurrence relationships among bacterioplankton communities in 35 surface water samples collected from Hulun Lake (a grassland-type lake), Wuliangsuhai Lake (an irrigated agricultural recession type lake), and Daihai Lake (an inland lake with mixed farming and grazing) in the Inner Mongolia Plateau, China. The results indicated a significant geographical distance decay pattern, with biomarkers (Proteobacteria and Bacteroidota) exhibiting differences in the contributions of different bacteria branches to the lakes. The relative abundance of Proteobacteria (42.23%) were high in Hulun Lake and Wuliangsuhai Lake. Despite Actinobacteriota was most dominant, Firmicutes accounted for approximately 17.07% in Daihai Lake, suggested the potential detection of anthropogenic impacts on bacteria within the agro-pastoral inland lake. Lake heterogeneity caused bacterioplankton responses to phosphorus, chlorophyll a, and salinity in Hulun Lake, Wuliangsuhai Lake, and Daihai Lake. Although bacterioplankton community assembly processes in irrigated agricultural recession type lake were more affected by dispersal limitation than those in grassland-type lake and inland lake with mixed farming and grazing (approximately 52.7% in Hulun Lake), dispersal limitation and undominated processes were key modes of bacterioplankton community assembly in three lakes. This suggested stochastic processes exerted a greater impact on bacterioplankton community assembly in a typical Inner Mongolia Lake than deterministic processes. Overall, the bacterioplankton communities displayed the potential for collaboration, with lowest connectivity observed in irrigated agricultural recession type lake, which reflected the complex dynamic patterns of aquatic bacteria in typical Inner Mongolia Plateau lakes. These findings enhanced our understanding of the interspecific relationships and assembly processes among microorganisms in lakes with distinct habitats.
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Affiliation(s)
- Yujiao Shi
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenbao Li
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China; Inner Mongolia Key Laboratory of Protection and Utilization of Water Resources, Hohhot, 010018, China.
| | - Xin Guo
- Water Conservancy and Civil Engineering College, Inner Mongolia Agricultural University, Hohhot, 010018, China
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2
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Adams KS, Finaughty DA, Gibbon VE. Forensic taphonomic experimental design matters: a study assessing clothing and carrion biomass load on scavenging in Cape Town, South Africa. Int J Legal Med 2024; 138:1669-1684. [PMID: 38374286 PMCID: PMC11164742 DOI: 10.1007/s00414-024-03171-w] [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: 09/15/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
The identification of unknown human remains is a significant and ongoing challenge in South Africa, worsened by the country's high murder rate. The rate of decomposition in South Africa is significantly influenced by vertebrate scavenging, which, if not considered, can impede the accurate estimation of the post-mortem interval. Scavenging patterns vary greatly depending on the environment and ecological region, and there is limited data for the Western Cape province. To address this gap, two clothed and uncaged pig carcasses weighing 60 kg each were placed in the field in July 2021 and January 2022, respectively. Motion-activated infrared-capable trail cameras were used to observe decomposition, scavenger species, and their activities. Additionally, a comparative sample of 16 unclothed carcasses deployed between 2014 and 2016 in the same habitat were analyzed to assess the impact of clothing and biomass load. The study found three main results: (1) Regardless of habitat or biomass load, it took significantly less time to reach decomposition milestones (25%, 50%, and 75%) during the summer season; (2) the presence of mongoose scavengers had a greater impact on the time required to reach milestones during winter compared to summer; and (3) single carcass deployments reached the milestones faster than multi-carcass deployments in both seasons. This research highlights the potential inaccuracy of current methods for estimating the post-mortem interval when scavenging activity is not considered or documented in the underlying experimental data, particularly for environments or ecological biomes where scavengers actively impact decomposition rates.
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Affiliation(s)
- Kara Sierra Adams
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Anatomy Building, Level 5, Room 5.14, Faculty of Health Sciences, University of Cape Town, , Anzio Rd, Observatory, Cape Town, 7925, South Africa
| | - Devin Alexander Finaughty
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Anatomy Building, Level 5, Room 5.14, Faculty of Health Sciences, University of Cape Town, , Anzio Rd, Observatory, Cape Town, 7925, South Africa
- School of Chemistry and Forensic Science, Division of Natural Sciences, University of Kent, Canterbury, Kent, UK
| | - Victoria Elaine Gibbon
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, Anatomy Building, Level 5, Room 5.14, Faculty of Health Sciences, University of Cape Town, , Anzio Rd, Observatory, Cape Town, 7925, South Africa.
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Gillmann SM, Lorenz AW, Kaijser W, Nguyen HH, Haase P, Hering D. How tolerances, competition and dispersal shape benthic invertebrate colonisation in restored urban streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172665. [PMID: 38653408 DOI: 10.1016/j.scitotenv.2024.172665] [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: 12/15/2023] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Biotic communities often respond poorly to river restoration activities and the drivers of community recovery after restoration are not fully understood. According to the Asymmetric Response Concept (ARC), dispersal capacity, species tolerances to stressors, and biotic interactions are three key drivers influencing community recovery of restored streams. However, the ARC remains to be tested. Here we used a dataset on benthic invertebrate communities of eleven restored stream sections in a former open sewer system that were sampled yearly over a period of eleven years. We applied four indices that reflect tolerance against chloride and organic pollution, the community's dispersal capacity and strength of competition to the benthic invertebrate taxa lists of each year and site. Subsequently, we used generalised linear mixed models to analyse the change of these indices over time since restoration. Dispersal capacity was high directly after restoration but continuously decreased over time. The initial communities thus consisted of good dispersers and were later joined by more slowly dispersing taxa. The tolerance to organic pollution also decreased over time, reflecting continuous improvement of water quality and an associated increase of sensitive species. On the contrary, chloride tolerances did not change, which could indicate a stable chloride level throughout the sampling period. Lastly, competition within the communities, reflected by interspecific trait niche overlap, increased with time since restoration. We show that recovery follows a specific pattern that is comparable between sites. Benthic communities change from tolerant, fast dispersing generalists to more sensitive, slowly dispersing specialists exposed to stronger competition. Our results lay support to the ARC (increasing role of competition, decreasing role of dispersal) but also underline that certain tolerances may still shape communities a decade after restoration. Disentangling the drivers of macroinvertebrate colonisation can help managers to better understand recovery trajectories and to define more realistic restoration targets.
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Affiliation(s)
- Svenja M Gillmann
- Department of Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
| | - Armin W Lorenz
- Department of Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Willem Kaijser
- Department of Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Hong Hanh Nguyen
- Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Peter Haase
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany; Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Daniel Hering
- Department of Aquatic Ecology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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4
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Tian K, Chen S, Ye R, Xie Y, Yao L, Lin H. Initial microbiome and tree root status structured the soil microbial community discrepancy of the subtropical pine-oak forest in a large urban forest park. Front Microbiol 2024; 15:1391863. [PMID: 38881652 PMCID: PMC11176443 DOI: 10.3389/fmicb.2024.1391863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/06/2024] [Indexed: 06/18/2024] Open
Abstract
Plant-microbe-soil interactions control over the forest biogeochemical cycling. Adaptive plant-soil interactions can shape specific microbial taxa in determining the ecosystem functioning. Different trees produce heterogeneous soil properties and can alter the composition of soil microbial community, which is relevant to the forest internal succession containing contrasting stand types such as the pine-oak forests. Considering representative microbial community characteristics are recorded in the original soil where they had adapted and resided, we constructed a soil transplant incubation experiment in a series of in situ root-ingrowth cores in a subtropical pine-oak forest, to simulate the vegetational pine-oak replacement under environmental succession. The responsive bacterial and fungal community discrepancies were studied to determine whether and how they would be changed. The pine and oak forest stands had greater heterogeneity in fungi composition than bacteria. Original soil and specific tree root status were the main factors that determined microbial community structure. Internal association network characters and intergroup variations of fungi among soil samples were more affected by original soil, while bacteria were more affected by receiving forest. Specifically, dominant tree roots had strong influence in accelerating the fungi community succession to adapt with the surrounding forest. We concluded that soil microbial responses to forest stand alternation differed between microbiome groups, with fungi from their original forest possessing higher resistance to encounter a new vegetation stand, while the bacteria community have faster resilience. The data would advance our insight into local soil microbial community dynamics during ecosystem succession and be helpful to enlighten forest management.
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Affiliation(s)
- Kai Tian
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Shaoming Chen
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Rumeng Ye
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Yanghe Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Lunguang Yao
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Hong Lin
- School of Food Science, Institute of Applied Ecology, Nanjing Xiaozhuang University, Nanjing, China
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5
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Smith SK, Weaver JE, Ducoste JJ, de Los Reyes FL. Microbial community assembly in engineered bioreactors. WATER RESEARCH 2024; 255:121495. [PMID: 38554629 DOI: 10.1016/j.watres.2024.121495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/10/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.
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Affiliation(s)
- Savanna K Smith
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA
| | - Joseph E Weaver
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Joel J Ducoste
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA
| | - Francis L de Los Reyes
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA.
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6
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Jing Z, Tu S, Yuan P, Liu X, Wang S, Dong B, Li Q, Gao H. The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133673. [PMID: 38340561 DOI: 10.1016/j.jhazmat.2024.133673] [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: 07/17/2023] [Revised: 12/17/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.
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Affiliation(s)
- Zhangmu Jing
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Shengqiang Tu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Peng Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Xiaoling Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Siyu Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Bin Dong
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Qingqian Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Hongjie Gao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China; State Environmental Protection Key Laboratory of Estuarine and Coastal Environment, Chinese Research Academy of Environmental Science, Beijing 100012, PR China.
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7
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Xu Y, Ge LL, Cheng XF, Xiang XL, Wen XL, Wang YJ, Fu H, Ge YL, Xi YL. Temporal Distribution Patterns of Cryptic Brachionus calyciflorus (Rotifera) Species in Relation to Biogeographical Gradient Associated with Latitude. Animals (Basel) 2024; 14:244. [PMID: 38254413 PMCID: PMC10812649 DOI: 10.3390/ani14020244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Sympatric distribution and temporal overlap of cryptic zooplankton species pose a challenge to the framework of the niche differentiation theory and the mechanisms allowing competitor coexistence. We applied the methods of phylogenetic analysis, DNA taxonomy, and statistical analysis to study the temporal distribution patterns of the cryptic B. calyciflorus species, an excellent model, in three lakes, and to explore the putative mechanisms for their seasonal succession and temporal overlap. The results showed that in the warm-temperate Lake Yunlong, B. fernandoi and B. calyciflorus s.s. underwent a seasonal succession, which was largely attributed to their differential adaptation to water temperature. In the subtropical Lake Jinghu, B. fernandoi, B. calyciflorus s.s., and B. dorcas exhibited both seasonal succession and temporal overlap. Seasonal successions were largely attributed to their differential adaptation to temperature, and temporal overlap resulted from their differential responses to algal food concentration. In the tropical Lake Jinniu, B. calyciflorus s.s. persisted throughout the year and overlapped with B. dorcas for 5 months. The temporal overlap resulted from their differential responses to copepod predation. These results indicated that the temporal distribution pattern of the cryptic B. calyciforus species and the mechanism that allows competitor coexistence vary with different climate zones.
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Affiliation(s)
- Yuan Xu
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Le-Le Ge
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Xin-Feng Cheng
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Xian-Ling Xiang
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Xin-Li Wen
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Yong-Jin Wang
- Management Committee of Scenic Attraction of Lake Yunlong, Xuzhou 221007, China;
| | - Hao Fu
- Reservoir Management Office of Lake Yunlong, Xuzhou 221007, China;
| | - Ya-Li Ge
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
| | - Yi-Long Xi
- School of Ecology and Environment, Anhui Normal University, Wuhu 241002, China; (Y.X.); (L.-L.G.); (X.-F.C.); (X.-L.X.); (X.-L.W.)
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Funded by Anhui Province and Ministry of Education of the People’s Republic of China, Anhui Normal University, Wuhu 241002, China
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8
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Grether GF, Finneran AE, Drury JP. Niche differentiation, reproductive interference, and range expansion. Ecol Lett 2024; 27:e14350. [PMID: 38062899 DOI: 10.1111/ele.14350] [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: 08/28/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 01/31/2024]
Abstract
Understanding species distributions and predicting future range shifts requires considering all relevant abiotic factors and biotic interactions. Resource competition has received the most attention, but reproductive interference is another widespread biotic interaction that could influence species ranges. Rubyspot damselflies (Hetaerina spp.) exhibit a biogeographic pattern consistent with the hypothesis that reproductive interference has limited range expansion. Here, we use ecological niche models to evaluate whether this pattern could have instead been caused by niche differentiation. We found evidence for climatic niche differentiation, but the species that encounters the least reproductive interference has one of the narrowest and most peripheral niches. These findings strengthen the case that reproductive interference has limited range expansion and also provide a counterexample to the idea that release from negative species interactions triggers niche expansion. We propose that release from reproductive interference enables species to expand in range while specializing on the habitats most suitable for breeding.
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Affiliation(s)
- Gregory F Grether
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Ann E Finneran
- Department of Ecology & Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
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9
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Premate E, Kepic T, Fišer C. Is the relationship between body length and body mass consistent across habitats? A case study on Niphargus (Crustacea: Amphipoda). ZOOLOGY 2023; 161:126120. [PMID: 37696118 DOI: 10.1016/j.zool.2023.126120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Body size is one of the main characteristics of any organism and influences various aspects of individual's biology. In animal ecology, it represents a key functional trait that can be quantified using different measures and is often used as a proxy for different organismal functions. The way we quantify body size is critical in any study using this measure alone or to scale other organismal traits. It is especially important in groups that act as model systems across different fields of biological research. One of such groups are amphipods, which are at focus in many ecological studies where appropriate quantification of body size is needed. Here, we explored the relationship between body length and body mass in the largest freshwater amphipod genus Niphargus, and evaluated whether the two measures lead to different conclusions in a putative ecological study of species coexistence. We selected 16 species inhabiting two different subterranean habitats, cave lakes and cave streams. The relationship between log-transformed body mass and body length was linear in all species, but body mass increased steeper among species from cave lakes than from cave streams, reflecting the stouter body shape of the former. In the simulated ecological study, the comparisons of the two measures showed that they may yield different results: in 10 % of cases, body length detected differences between species when body mass did not and vice versa (13 %). Usage of body length or body mass can thus lead to different conclusions. We recommend avoiding direct transformations between body length and body mass in ecological studies. Whenever needed, such transformations should be done with caution using habitat-specific body mass - body length ratios.
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Affiliation(s)
- Ester Premate
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBio Lab, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| | - Tinkara Kepic
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBio Lab, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Cene Fišer
- University of Ljubljana, Biotechnical Faculty, Department of Biology, SubBio Lab, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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10
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Masciocchi M, Mattiacci A, Villacide JM, Buteler M, Porrino AP, Martínez AS. Sugar responsiveness could determine foraging patterns in yellowjackets. Sci Rep 2023; 13:20448. [PMID: 37993633 PMCID: PMC10665408 DOI: 10.1038/s41598-023-47819-w] [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: 09/14/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023] Open
Abstract
Sympatric-related species often exhibit resource partitioning. This can occur through different mechanisms, such as behavioral, morphological, and sensory variations, leading to qualitative, temporal, or spatial differences in resource exploitation, such as consuming different types of food. Sensory-based niche partitioning could be the underlying mechanism through which closely related species effectively reduce niche overlap. Here we ask whether variations in sensory responses to carbohydrates could reflect differences in the foraging patterns of two Vespula species present in Patagonia. For this, we established (i) the response thresholds toward carbohydrate solutions of foraging V. germanica and V. vulgaris in the laboratory, (ii) the sugar concentration of foraged carbohydrates in the field, and (iii) possible effects of incoming sugar concentration and performance at individual and colony levels. Results indicate a higher sucrose response threshold in V. germanica than V. vulgaris. Field results indicate that higher carbohydrate concentrations foraged by V. germanica, with 57% of V. germanica foragers returning with concentrations above 50% w/w, while only 23% of V. vulgaris foragers did so. These differences in sucrose sensitivity and foraging patterns positively correlate with colony size, irrespective of the species. Our results suggest that competition could be reduced in these closely related invasive social wasp species through sensory differences in their sugar perception levels, which would lead to them foraging different carbohydrate sources. This study suggests that sensory niche partitioning could promote species coexistence in these social wasps.
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Affiliation(s)
- Maité Masciocchi
- Grupo de Ecología de Poblaciones de Insectos, IFAB - Instituto de Investigaciones Forestales y Agropecuarias Bariloche (INTA - CONICET), Bariloche, Argentina
| | - Analía Mattiacci
- Grupo de Ecología de Poblaciones de Insectos, IFAB - Instituto de Investigaciones Forestales y Agropecuarias Bariloche (INTA - CONICET), Bariloche, Argentina
| | - José M Villacide
- Grupo de Ecología de Poblaciones de Insectos, IFAB - Instituto de Investigaciones Forestales y Agropecuarias Bariloche (INTA - CONICET), Bariloche, Argentina
| | - Micaela Buteler
- INIBIOMA - Instituto de Investigaciones en Biodiversidad y Medioambiente (CONICET - UN Comahue), Bariloche, Argentina
| | - Agustina P Porrino
- Grupo de Ecología de Poblaciones de Insectos, IFAB - Instituto de Investigaciones Forestales y Agropecuarias Bariloche (INTA - CONICET), Bariloche, Argentina
| | - Andrés S Martínez
- Grupo de Ecología de Poblaciones de Insectos, IFAB - Instituto de Investigaciones Forestales y Agropecuarias Bariloche (INTA - CONICET), Bariloche, Argentina.
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11
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Hu Y, Zhang J, Wang Y, Hu S. Distinct mechanisms shape prokaryotic community assembly across different land-use intensification. WATER RESEARCH 2023; 245:120601. [PMID: 37708774 DOI: 10.1016/j.watres.2023.120601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Changes in land-use intensity can have a far-reaching impact on river water quality and prokaryotic community composition. While research has been conducted to investigate the assembly mechanism of prokaryotic communities, the contributions of neutral theory and niche theory to prokaryotic community assembly under different land-use intensities remain unknown. In this study, a total of 251 sampling sites were set up in the Yangtze River basin to explore the assembly mechanism under different land-use intensities. Briefly, a "source" landscape can generate pollution, whereas a "sink" landscape can prevent pollution. Firstly, our result showed that higher land-use intensity might disturb the balance between the "source" and "sink" landscape patterns, resulting in water quality deterioration. Then the prokaryotic community assembly was classified into five ecological processes, namely homogeneous selection, homogenizing dispersal, undominated processes, dispersal limitation, and variable selection. The higher land-use intensity was found to strengthen the homogeneous selection, leading to the homogenization of the community at the whole basin scale. Finally, our findings demonstrated that the Yangtze River Basin's prokaryotic community displayed a distance-decay pattern when land-use intensity was low, with a greater contribution from neutral theory to its assembly. On the other hand, with a higher land-use intensity, the degradation of the aquatic environment increased the impacts of environmental filtering on the prokaryotic community, and niche theory played a stronger role in its assembly. Our findings show how land-use intensity influence the formation of prokaryotic communities, which will be an invaluable guide for managing land use and understanding the prokaryotic community assembly mechanisms in the Yangtze River Basin.
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Affiliation(s)
- Yuxin Hu
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China.
| | - Jing Zhang
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China
| | - Yingcai Wang
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China.
| | - Sheng Hu
- Yangtze River Basin Ecological Environment Monitoring and Scientific Research Center, Yangtze River Basin Ecological Environment Supervision and Administration Bureau, Ministry of Ecology and Environment, Wuhan 430010, Hubei, China.
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12
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Wu L, Yang Y, Ning D, Gao Q, Yin H, Xiao N, Zhou BY, Chen S, He Q, Zhou J. Assessing mechanisms for microbial taxa and community dynamics using process models. MLIFE 2023; 2:239-252. [PMID: 38817815 PMCID: PMC10989933 DOI: 10.1002/mlf2.12076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/27/2023] [Accepted: 05/27/2023] [Indexed: 06/01/2024]
Abstract
Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer-resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer-resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.
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Affiliation(s)
- Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental SciencesPeking UniversityBeijingChina
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Daliang Ning
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Huaqun Yin
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Naija Xiao
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
| | - Benjamin Y. Zhou
- Department of Mathematics, Lunt HallNorthwestern UniversityEvanstonIllinoisUSA
| | - Si Chen
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
- Institute for a Secure and Sustainable EnvironmentThe University of TennesseeKnoxvilleTennesseeUSA
| | - Qiang He
- Department of Civil and Environmental EngineeringThe University of TennesseeKnoxvilleTennesseeUSA
- Institute for a Secure and Sustainable EnvironmentThe University of TennesseeKnoxvilleTennesseeUSA
| | - Jizhong Zhou
- Institute for Environmental GenomicsUniversity of OklahomaNormanOKUSA
- Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOKUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- School of Computer ScienceUniversity of OklahomaNormanOKUSA
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13
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Loke LHL, Chisholm RA. Unveiling the transition from niche to dispersal assembly in ecology. Nature 2023:10.1038/s41586-023-06161-x. [PMID: 37286612 DOI: 10.1038/s41586-023-06161-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a 'niche detector' and a tool for assessing when communities are niche versus dispersal assembled.
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Affiliation(s)
- Lynette H L Loke
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, New South Wales, Australia.
| | - Ryan A Chisholm
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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14
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Qiao Y, Hou D, Lin Z, Wei S, Chen J, Li J, Zhao J, Xu K, Lu L, Tian S. Sulfur fertilization and water management ensure phytoremediation coupled with argo-production by mediating rhizosphere microbiota in the Oryza sativa L.-Sedum alfredii Hance rotation system. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131686. [PMID: 37270958 DOI: 10.1016/j.jhazmat.2023.131686] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/22/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Sulfur (S) fertilizers, water management and crop rotation are important agronomic practices, related to soil heavy metal bioavailability. However, the mechanisms of microbial interactions remain unclear. Herein, we investigated how S fertilizers (S0 and Na2SO4) and water management affected plant growth, soil cadmium (Cd) bioavailability, and rhizospheric bacterial communities in the Oryza sativa L. (rice)-Sedum alfredii Hance (S. alfredii) rotation system through 16S rRNA gene sequencing and ICP-MS analysis. During rice cultivation, continuous flooding (CF) was better than alternating wetting and drying (AWD). CF treatment decreased soil Cd bioavailability by the promotion of insoluble metal sulfide production and soil pH, thus lowering Cd accumulation in grains. S application recruited more S-reducing bacteria in the rhizosphere of rice, whilst Pseudomonas promoted metal sulfide production and rice growth. During S. alfredii cultivation, S fertilizer recruited S-oxidizing and metal-activating bacteria in the rhizosphere. Thiobacillus may oxidize metal sulfides and enhance Cd and S absorption into S. alfredii. Notably, S oxidation decreased soil pH and elevated Cd content, thereby promoting S. alfredii growth and Cd absorption. These findings showed rhizosphere bacteria were involved in Cd uptake and accumulation in the rice-S. alfredii rotation system, thus providing useful information for phytoremediation coupled with argo-production.
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Affiliation(s)
- Yabei Qiao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Zhi Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Shuai Wei
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jiuzhou Chen
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jiahao Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Kuan Xu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Lingli Lu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Shengke Tian
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China.
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15
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Wang X, Han Q, Yu Q, Wang S, Yang J, Su W, Wan-Yan R, Sun X, Li H. Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil. ENVIRONMENTAL RESEARCH 2023; 225:115653. [PMID: 36898422 DOI: 10.1016/j.envres.2023.115653] [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: 01/03/2023] [Revised: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.
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Affiliation(s)
- Xiaochen Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Ruijun Wan-Yan
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiaofang Sun
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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16
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Norberg A, Susi H, Sallinen S, Baran P, Clark NJ, Laine AL. Direct and indirect viral associations predict coexistence in wild plant virus communities. Curr Biol 2023; 33:1665-1676.e4. [PMID: 37019108 DOI: 10.1016/j.cub.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/17/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023]
Abstract
Viruses are a vastly underestimated component of biodiversity that occur as diverse communities across hierarchical scales from the landscape level to individual hosts. The integration of community ecology with disease biology is a powerful, novel approach that can yield unprecedented insights into the abiotic and biotic drivers of pathogen community assembly. Here, we sampled wild plant populations to characterize and analyze the diversity and co-occurrence structure of within-host virus communities and their predictors. Our results show that these virus communities are characterized by diverse, non-random coinfections. Using a novel graphical network modeling framework, we demonstrate how environmental heterogeneity influences the network of virus taxa and how the virus co-occurrence patterns can be attributed to non-random, direct statistical virus-virus associations. Moreover, we show that environmental heterogeneity changed virus association networks, especially through their indirect effects. Our results highlight a previously underestimated mechanism of how environmental variability can influence disease risks by changing associations between viruses that are conditional on their environment.
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Affiliation(s)
- Anna Norberg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland; Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7034 Trondheim, Norway.
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Pezhman Baran
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Nicholas J Clark
- School of Veterinary Science, Faculty of Science, University of Queensland, Gatton, QL 4343, Australia
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
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17
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Qu S, Shen C, Zhang L, Wang J, Zhang LM, Chen B, Sun GX, Ge Y. Dispersal limitation and host selection drive geo-specific and plant-specific differentiation of soil bacterial communities in the Tibetan alpine ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160944. [PMID: 36526178 DOI: 10.1016/j.scitotenv.2022.160944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soil bacteria, which are active in shrub encroachment, play key roles in regulating ecosystem structure and function. However, the differentiation characteristics and assembly process of bacterial communities in scrubbed grasslands remain unknown. Taking the Qinghai-Tibet Plateau, a hotspot of shrub encroachment, as the study area, we collected 192 soils near nine natural typical shrubs' roots on a trans-longitude transect (about 1800 km) and investigated the bacterial communities using 16S rRNA amplicon sequencing. We found that the bacterial communities exhibited plant-specific and geographic-specific differentiation. On the one hand, bacterial communities differed significantly across plant species, with widely distributed shrubs harboring high diversity communities but few plant-specific taxa, and narrowly distributed shrubs possessing low diversity communities but more plant-specific taxa. Besides, there was a significant negative correlation between bacterial community similarity and plant phylogenetic distance. On the other hand, bacterial communities differed across geographic sites, with a significant decay in bacterial community similarity with geographic distance. The bacterial alpha diversity varied in an inverted V-shape from west to east, peaking at 91°E, which could be largely driven by mean annual temperature, soil pH and soil total carbon content. Community differentiation increased with the heterogeneity degree of assembly processes, and the dominant assembly process in these two specific differentiations differed. Dominated by stochastic and deterministic forces, respectively, geography diverged bacterial communities primarily through increased dispersal limitation, whereas plants diverged bacterial communities primarily through increased variable selection. Our study provides new insight into the characteristics and mechanisms of root-surrounding soil bacteria differentiation in scrubbed grasslands, contributing to the scientific management of degraded grasslands and the prediction of bacterial community structure and ecosystem function in response to global change.
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Affiliation(s)
- Sai Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guo-Xin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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18
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Bontemps Z, Hugoni M, Moënne-Loccoz Y. Microscale dynamics of dark zone alterations in anthropized karstic cave shows abrupt microbial community switch. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160824. [PMID: 36502978 DOI: 10.1016/j.scitotenv.2022.160824] [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: 10/28/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Strong anthropization of karstic caves may result in formation of various wall alterations including dark zones, whose microbial community differs from that of non-altered surfaces nearby. Dark zones grow quickly and without gradual visual changes, leading to the hypothesis of a simple process rather than complex microbial successions, but this is counter-intuitive as underground microbial changes are typically slow and dark zones are microbiologically very distinct from unmarked surfaces. We tested this hypothesis in Paleolithic Lascaux Cave, across two years of microscale sampling. Indeed, Illumina MiSeq metabarcoding evidenced only three community stages for bacteria, fungi and all microeukaryotes together (i.e. unmarked surfaces, newly-formed dark zones and intermediate/old dark zones) and just two stages for archaea (unmarked surfaces vs dark zones), indicating abrupt community changes. The onset of dark zone formation coincided with the development of Ochroconis fungi, Bacteroidota and the bacterial genera Labrys, Nonomuraea and Sphingomonas, in parallel to Pseudomonas counter-selection. Modeling of community assembly processes highlighted that the dynamics of rare taxa in unmarked surfaces adjacent to dark zones and in newly-formed dark zones were governed in part by deterministic processes. This suggests that cooperative relationships between these taxa might be important to promote dark zone formation. Taken together, these findings indicate an abrupt community switch as these new alterations form on Lascaux cave walls.
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Affiliation(s)
- Zélia Bontemps
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France; Univ Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, F-69621 Villeurbanne, France; Institut Universitaire de France (IUF), France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.
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19
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Barrero A, Ovaskainen O, Traba J, Gómez‐Catasús J. Co‐occurrence patterns in a steppe bird community: insights into the role of dominance and competition. OIKOS 2023. [DOI: 10.1111/oik.09780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- Adrián Barrero
- Terrestrial Ecology Group, Dept of Ecology, Univ. Autónoma de Madrid (TEG-UAM) Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Univ. Autónoma de Madrid (CIBC‐UAM) Madrid Spain
| | - Otso Ovaskainen
- Dept of Biological and Environmental Science, Univ. of Jyväskylä Jyväskylä Finland
- Organismal and Evolutionary Biology Research Program, Univ. of Helsinki Helsinki Finland
| | - Juan Traba
- Terrestrial Ecology Group, Dept of Ecology, Univ. Autónoma de Madrid (TEG-UAM) Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Univ. Autónoma de Madrid (CIBC‐UAM) Madrid Spain
| | - Julia Gómez‐Catasús
- Terrestrial Ecology Group, Dept of Ecology, Univ. Autónoma de Madrid (TEG-UAM) Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global, Univ. Autónoma de Madrid (CIBC‐UAM) Madrid Spain
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20
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Fang J, Tao Y, Liu J, Lyu T, Yang X, Ma S, Dong J, Dou H, Zhang H. Effects of emergent plants on soil carbon-fixation and denitrification processes in freshwater and brackish wetlands in a watershed in northern China. GEODERMA 2023; 430:116311. [DOI: 10.1016/j.geoderma.2022.116311] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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21
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Jospin A, Chittaro Y, Bolt D, Demergès D, Gurcel K, Hensle J, Sanchez A, Praz C, Lucek K. Genomic evidence for three distinct species in the Erebia manto complex in Central Europe (Lepidoptera, Nymphalidae). CONSERV GENET 2023; 24:293-304. [PMID: 37187800 PMCID: PMC10175325 DOI: 10.1007/s10592-023-01501-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
Abstract
A problem to implement conservation strategies is that in many cases recognized taxa are in fact complexes of several cryptic species. Failure to properly delineate species may lead to misplaced priorities or to inadequate conservation measures. One such species complex is the yellow-spotted ringlet Erebia manto, which comprises several phenotypically distinct lineages, whose degree of genomic isolation has so far not been assessed. Some of these lineages are geographically restricted and thus possibly represent distinct units with conservation priorities. Using several thousand nuclear genomic markers, we evaluated to which degree the bubastis lineage from the Alps and the vogesiaca lineage from the Vosges, are genetically isolated from the widespread manto lineage. Our results suggest that both lineages are genetically as strongly differentiated from manto as other taxonomically well separated sibling species in this genus from each other, supporting a delineation of bubastis and vogesiaca as independent species. Given the restricted and isolated range of vogesiaca as well as the disjunct distribution of bubastis, our findings have significant implication for future conservation efforts on these formerly cryptic species and highlight the need to investigate the genomic identity within species complexes. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-023-01501-w.
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Affiliation(s)
- Amanda Jospin
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | | | | | - David Demergès
- Conservatoire d’espaces Naturels de Lorraine, 20 Chemin de L’école Des Xettes, 88400 Gérardmer, France
| | | | | | - Andreas Sanchez
- Info Fauna, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Christophe Praz
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Info Fauna, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, 4056 Basel, Switzerland
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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22
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Ma S, Geng H, Yan C, Han X, Xu D, Zhao F, Blake RE, Zhou B, Chen H, Yuan R, Jin B, Liu H, Wang F. Nutrient dynamics and microbial community response in macrophyte-dominated lakes: Implications for improved restoration strategies. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116372. [PMID: 36252327 DOI: 10.1016/j.jenvman.2022.116372] [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: 06/30/2022] [Revised: 08/28/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Although lakes dominated by macrophytes are conducive to ecological balance, this balance is easily disrupted by excessive nutrients flowing into the lake. However, knowledge of whether excessive nutrients lead to different microbial environmental vulnerabilities in the lake sediment between macrophyte-dominated areas and macrophyte-free areas is a prerequisite for the implementation of targeted protection measures. In this study, we investigated bacterial communities in sediments using high-throughput sequencing of 16S rRNA genes. Our results showed that the sources of total nitrogen (TN) and organic matter (OM) were related to the macrophytes. The structure, drivers, and interspecific associations of bacterial community, which were more susceptible to increased changes in TN and OM, differed significantly between macrophyte-dominated areas and macrophyte-free areas. More precisely, the lake edge, where was occupied by macrophytes, had a higher proportion of deterministic phylogenetic turnover (88.89%) than other sites, as well as a wider ecological niche and a tighter network structure. Further, as the difference in TN increased, the main assembly processes in surface sediments changed from stochastic to deterministic. However, the majority of phyla from the lake edge showed a greater correlation with excessive nutrients, and the selection of the community by excessive nutrients was more obvious at the edge of the lake. In addition, our results demonstrated that the stability of the bacterial community in macrophyte-free areas is greater than in macrophyte-dominated areas, while an excessively high deterministic process ratio and nutrient (TN and OM) concentration significantly reduced bacterial community stability at macrophyte-dominated areas. Taken together, these results provide a better understanding of the effects of excessive nutrients derived from macrophytes on bacterial community patterns, and highlight the importance of avoiding the accumulation of TN and OM in macrophyte-dominated areas to enhance the sustainability of the ecosystem after restoration of lakes with macrophytes.
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Affiliation(s)
- Shuai Ma
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China; School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China
| | - Huanhuan Geng
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Changchun Yan
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Xiaomin Han
- Shunyi District Water Authority, 3 Fuxing East Road, Shunyi District, Beijing, 101300, PR China
| | - Dan Xu
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Furong Zhao
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Ruth E Blake
- Department of Earth and Planetary Sciences, Yale University, 210 Whitney Ave, New Haven, CT 06511, USA
| | - Beihai Zhou
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Huilun Chen
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Rongfang Yuan
- School of Energy & Environmental Engineering, And Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Baoshi Jin
- School of Resources and Environment, Anqing Normal University, 1318 Jixian North Road, Anqing, Anhui, 246133, PR China
| | - Haijun Liu
- School of Resources and Environment, Anqing Normal University, 1318 Jixian North Road, Anqing, Anhui, 246133, PR China.
| | - Fei Wang
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing, 100875, PR China.
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23
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Kiemel K, Gurke M, Paraskevopoulou S, Havenstein K, Weithoff G, Tiedemann R. Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species. Sci Rep 2022; 12:22626. [PMID: 36587065 PMCID: PMC9805463 DOI: 10.1038/s41598-022-27137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/26/2022] [Indexed: 01/01/2023] Open
Abstract
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
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Affiliation(s)
- K. Kiemel
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - M. Gurke
- grid.422371.10000 0001 2293 9957Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany ,grid.7468.d0000 0001 2248 7639Department of Biology, Humboldt-University, Invalidenstraße 42, 10115 Berlin, Germany
| | - S. Paraskevopoulou
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Microbiology Group, Sölvegatan 35, 223 62 Lund, Sweden
| | - K. Havenstein
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
| | - G. Weithoff
- grid.11348.3f0000 0001 0942 1117Unit of Ecology and Ecosystem Modelling, Institute for Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
| | - R. Tiedemann
- grid.11348.3f0000 0001 0942 1117Unit of Evolutionary Biology/Systematic Zoology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht Straße 24-25, 14476 Potsdam, Germany
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24
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Jewell MD, Bell G. A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities. Ecol Evol 2022; 12:e9568. [PMID: 36479026 PMCID: PMC9720002 DOI: 10.1002/ece3.9568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/25/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Community dynamics are governed by two opposed processes: species sorting, which produces deterministic dynamics leading to an equilibrium state, and ecological drift, which produces stochastic dynamics. Despite a great deal of theoretical and empirical work aiming to demonstrate the predominance of one or the other of these processes, the importance of drift in structuring communities and maintaining species diversity remains contested. Here, we present the results of a basic community dynamics experiment using floating aquatic plants, designed to measure the relative contributions of species sorting and ecological drift to community change over about a dozen generations. We found that species sorting became overwhelmingly dominant as the experiment progressed, and directed communities toward a stable equilibrium state maintained by negative frequency-dependent selection. The dynamics of any particular species depended on how far its initial frequency was from its equilibrium frequency, however, and consequently the balance of sorting and drift varied among species.
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Affiliation(s)
| | - Graham Bell
- Department of BiologyMcGill UniversityMontrealQuebecCanada
- Redpath MuseumMcGill UniversityMontrealQuebecCanada
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25
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Augustijnen H, Patsiou T, Lucek K. Secondary contact rather than coexistence-Erebia butterflies in the Alps. Evolution 2022; 76:2669-2686. [PMID: 36117267 PMCID: PMC9828779 DOI: 10.1111/evo.14615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/05/2022] [Accepted: 08/30/2022] [Indexed: 01/22/2023]
Abstract
Secondary contact zones are ideal systems to study the processes that govern the evolution of reproductive barriers, especially at advanced stages of the speciation process. An increase in reproductive isolation resulting from selection against maladaptive hybrids is thought to contribute to reproductive barrier buildup in secondary contact zones. Although such processes have been invoked for many systems, it remains unclear to which extent they influence contact zone dynamics in nature. Here, we study a very narrow contact zone between the butterfly species Erebia cassioides and Erebia tyndarus in the Swiss Alps. We quantified phenotypic traits related to wing shape and reproduction as well as ecology to compare the degree of intra- and interspecific differentiation. Even though only very few first-generation hybrids occur, we find no strong indications for current reinforcing selection, suggesting that if reinforcement occurred in our system, it likely operated in the past. Additionally, we show that both species differ less in their ecological niche at the contact zone than elsewhere, which could explain why coexistence between these butterflies may currently not be possible.
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Affiliation(s)
- Hannah Augustijnen
- Department of Environmental SciencesUniversity of BaselBaselCH‐4056Switzerland
| | - Theofania Patsiou
- Institute of Plant SciencesUniversity of BernBernCH‐3013Switzerland
- Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
| | - Kay Lucek
- Department of Environmental SciencesUniversity of BaselBaselCH‐4056Switzerland
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26
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Wang W, Jia T, Qi T, Li S, Degen AA, Han J, Bai Y, Zhang T, Qi S, Huang M, Li Z, Jiao J, Shang Z. Root exudates enhanced rhizobacteria complexity and microbial carbon metabolism of toxic plants. iScience 2022; 25:105243. [PMID: 36274956 PMCID: PMC9579507 DOI: 10.1016/j.isci.2022.105243] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Root exudates and rhizosphere microorganisms play key roles in the colonization of toxic plants under climate change and land degradation. However, how root exudates affect the rhizosphere microorganisms and soil nutrients of toxic plants in degraded grasslands remains unknown. We compared the interaction of soil microbial communities, root exudates, microbial carbon metabolism, and environmental factors in the rhizosphere of toxic and non-toxic plants. Deterministic processes had a greater effect on toxic than non-toxic plants, as root exudates affected rhizosphere microorganisms directly. The 328 up-regulated compounds in root exudates of toxic plants affected the diversity of rhizosphere microorganisms. Rhizosphere bacteria-enriched enzymes were involved in the phenylpropanoid biosynthesis pathway. Root exudates of toxic plants form complex networks of rhizosphere microorganisms, provide high rhizosphere nutrients, and increase microbial carbon metabolism. The interaction between root exudates and rhizosphere microorganisms is the key mechanism that enables toxic plants to spread in degraded grassland habitats.
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Affiliation(s)
- Wenyin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Tianhua Jia
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Tianyun Qi
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shanshan Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - A. Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel
| | - Jin Han
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yanfu Bai
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Tao Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shuai Qi
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mei Huang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Zihao Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Jianxin Jiao
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Zhanhuan Shang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
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27
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Isabwe A, Yao H, Zhang S, Jiang Y, Breed MF, Sun X. Spatial assortment of soil organisms supports the size-plasticity hypothesis. ISME COMMUNICATIONS 2022; 2:102. [PMID: 37938741 PMCID: PMC9723746 DOI: 10.1038/s43705-022-00185-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2023]
Abstract
The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and, therefore, are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies for urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode, and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift, and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for example, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models.
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Affiliation(s)
- Alain Isabwe
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China
| | - Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Shixiu Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Feng SW, Lu JL, Liang JL, Wu ZH, Yi X, Wen P, Li FL, Liao B, Jia P, Shu WS, Li JT. Functional Guilds, Community Assembly, and Co-occurrence Patterns of Fungi in Metalliferous Mine Tailings Ponds in Mainland China. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02121-6. [PMID: 36205737 DOI: 10.1007/s00248-022-02121-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Metalliferous mine tailings ponds are generally characterized by low levels of nutrient elements, sustained acidic conditions, and high contents of toxic metals. They represent one kind of extreme environments that are believed to resemble the Earth's early environmental conditions. There is increasing evidence that the diversity of fungi inhabiting mine tailings ponds is much higher than previously thought. However, little is known about functional guilds, community assembly, and co-occurrence patterns of fungi in such habitats. As a first attempt to address this critical knowledge gap, we employed high-throughput sequencing to characterize fungal communities in 33 mine tailings ponds distributed across 18 provinces of mainland China. A total of 5842 fungal phylotypes were identified, with saprotrophic fungi being the major functional guild. The predictors of fungal diversity in whole community and sub-communities differed considerably. Community assembly of the whole fungal community and individual functional guilds were primarily governed by stochastic processes. Total soil nitrogen and total phosphorus mediated the balance between stochastic and deterministic processes of the fungal community assembly. Co-occurrence network analysis uncovered a high modularity of the whole fungal community. The observed main modules largely consisted of saprotrophic fungi as well as various phylotypes that could not be assigned to known functional guilds. The richness of core fungal phylotypes, occupying vital positions in co-occurrence network, was positively correlated with edaphic properties such as soil enzyme activity. This indicates the important roles of core fungal phylotypes in soil organic matter decomposition and nutrient cycling. These findings improve our understanding of fungal ecology of extreme environments.
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Affiliation(s)
- Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Zhuo-Hui Wu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Ping Wen
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Feng-Lin Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Bin Liao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China.
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
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29
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McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. Virus Evol 2022; 8:veac095. [PMID: 36405340 PMCID: PMC9667876 DOI: 10.1093/ve/veac095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 09/30/2022] [Indexed: 07/22/2023] Open
Abstract
The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.
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Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Adrián D Zamfir
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Bisola M Babalola
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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30
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Li J, Li M, Zhao L, Sun X, Gao M, Sheng L, Bian H. Characteristics of soil carbon emissions and bacterial community composition in peatlands at different stages of vegetation succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156242. [PMID: 35643137 DOI: 10.1016/j.scitotenv.2022.156242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/09/2022] [Accepted: 05/22/2022] [Indexed: 05/16/2023]
Abstract
Microorganisms are important components of soil ecosystems and play an important role in material cycles. Northern peatlands are important ecosystems in middle-high latitude regions. In peatlands, different vegetation successions occur with changes in groundwater levels. The overall carbon emission of peat bogs is related to the carbon stability of the surrounding environment. Unraveling the assembly and distribution of bacterial communities at different succession stages in peatland is essential to understanding the soil nutrient cycle. In this study, we investigated the characteristics of soil carbon emissions and the composition of subsurface microorganisms under six different succession stages. The highest carbon emission was observed in mossy peatlands, and their soil enzyme activity was closely related to the aboveground vegetation cover type. The succession pattern of ground vegetation was the main driver of soil microorganisms. The abundance of the dominant Proteobacteria decreased with increasing soil depth, while the opposite trend was observed for Chloroflexi. Furthermore, the community structure of microorganisms became progressively simpler and looser as soil water content decreased. The bacterial alpha diversity was driven by soil dissolved organic carbon and Fe, and the beta diversity was driven mainly by soil water content. The bacteria presented a random distribution in a nutrient-rich soil environment and shifted to deterministic distribution with decreasing water and nutrient contents. The balance between taxonomic diversity and dispersal limitation mediates species coexistence in the soil microbiome. This study provides new insights into the soil environment at different stages of succession in peatlands.
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Affiliation(s)
- Jianwei Li
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Ming Li
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Liyuan Zhao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Xiaoqian Sun
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Minghao Gao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Lianxi Sheng
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China
| | - Hongfeng Bian
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Changchun 130117, China.
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Vieira TB, Da Silva LC, Oprea M, Mendes P, Pimenta VT, Brito D, Esbérard CEL, de Souza Aguiar LM, Ditchfield AD. Species Composition of Bats in Brazilian Restingas: Testing Environmental Versus Geographical Hypotheses for Community Composition. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2022.24.1.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Thiago B. Vieira
- Laboratório de Ecologia, Universidade Federal do Pará, Campus Altamira. Rua Coronel José Porfírio 2515, São Sebastião, 68372-040, Altamira, PA, Brazil
| | - Liriann C. Da Silva
- Laboratório de Ecologia, Universidade Federal do Pará, Campus Altamira. Rua Coronel José Porfírio 2515, São Sebastião, 68372-040, Altamira, PA, Brazil
| | - Monik Oprea
- Programa de Pós-graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Rodovia Goiânia-Nerópolis km 5, Campus II Itatiaia, 74001-970, Goiânia, GO, Brazil
| | - Poliana Mendes
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Pavillon Paul-Comtois, rue de l'Agriculture, Université Laval, Québec, G1V 0A6, Canada
| | - Vinícius Teixeira Pimenta
- Laboratório de Estudos de Quirópteros, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Avenida Marechal Campos 1468, Maruípe, 29040-090, Vitória, ES, Brazil
| | - Daniel Brito
- Programa de Pós-graduação em Ecologia e Evolução, Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Rodovia Goiânia-Nerópolis km 5, Campus II Itatiaia, 74001-970, Goiânia, GO, Brazil
| | - Carlos E. L. Esbérard
- Instituto de Biologia, Universidade Federal Rural do Estado do Rio de Janeiro, km 47 da antiga Rio-São Paulo, 23851-970, Seropédica, RJ, Brazil
| | - Ludmilla M. de Souza Aguiar
- Laboratório de Biologia e Conservação de Morcegos, Departamento de Zoologia, Universidade de Brasília, Campus Darcy Ribeiro s/n, 70910-900, Brasília, DF, Brazil
| | - Albert D. Ditchfield
- Laboratório de Estudos de Quirópteros, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Avenida Marechal Campos 1468, Maruípe, 29040-090, Vitória, ES, Brazil
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32
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Zhang F, Zhou Z, Xiao Y. Distinct community assembly and co‐existence of arbuscular mycorrhizal fungi and diazotrophs across large scale soil fertility to improve functions in alfalfa cultivation systems. Environ Microbiol 2022; 24:5277-5291. [DOI: 10.1111/1462-2920.16176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/11/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Fengge Zhang
- College of Agro‐grassland Science Nanjing Agricultural University Nanjing China
| | - Zhibo Zhou
- College of Agro‐grassland Science Nanjing Agricultural University Nanjing China
| | - Yan Xiao
- College of Agro‐grassland Science Nanjing Agricultural University Nanjing China
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33
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Interkingdom Plant–Soil Microbial Ecological Network Analysis under Different Anthropogenic Impacts in a Tropical Rainforest. FORESTS 2022. [DOI: 10.3390/f13081167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plants and their associated soil microorganisms interact with each other and form complex relationships. The effects of slash-and-burn agriculture and logging on aboveground plants and belowground microorganisms have been extensively studied, but research on plant–microbial interkingdom ecological networks is lacking. In this study, using old growth forest as a control, we used metagenomic data (ITS and 16S rRNA gene amplified sequences) and plant data to obtain interdomain species association patterns for three different soil disturbance types (slash-and-burn, clear cutting and selective cutting) in a tropical rainforest based on interdomain ecological network (IDEN) analysis. Results showed that the soil bacterial–fungal and plant–microbe ecological networks had different topological properties among the three forest disturbance types compared to old growth forest. More nodes, links, higher modularity and negative proportion were found in the selective cutting stand, indicating higher stability with increasing antagonistic relationships and niche differentiation. However, the area of slash-and-burn forest yield opposite results. Network module analysis indicated that different keystone species were found in the four forest types, suggesting alternative stable states among them. Different plant species had more preferential associations with specific fungal taxa than bacterial taxa at the genus level and plant–microbe associations lagged behind bacterial–fungal associations. Overall, compared with old growth forests, the bacterial–fungal and plant–microbe ecological networks in the slash-and-burn and clear cutting stands were simpler, while the network in the selective cutting stand was more complex. Understanding the relationships between aboveground plants and belowground microorganisms under differing disturbance patterns in natural ecosystems will help in better understanding the surrounding ecosystem functions of ecological networks.
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Shi J, Zuo Y, Qu W, Liu X, Fan Y, Cao P, Wang J. Stochastic processes shape the aggregation of free-living and particle-attached bacterial communities in the Yangtze River Estuary, China. J Basic Microbiol 2022; 62:1514-1525. [PMID: 35835725 DOI: 10.1002/jobm.202100666] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 11/05/2022]
Abstract
An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO4 3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.
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Affiliation(s)
- Jing Shi
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Yaqiang Zuo
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Wu Qu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Xuezhu Liu
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Yingping Fan
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Pinglin Cao
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
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Graco‐Roza C, Aarnio S, Abrego N, Acosta ATR, Alahuhta J, Altman J, Angiolini C, Aroviita J, Attorre F, Baastrup‐Spohr L, Barrera‐Alba JJ, Belmaker J, Biurrun I, Bonari G, Bruelheide H, Burrascano S, Carboni M, Cardoso P, Carvalho JC, Castaldelli G, Christensen M, Correa G, Dembicz I, Dengler J, Dolezal J, Domingos P, Erös T, Ferreira CEL, Filibeck G, Floeter SR, Friedlander AM, Gammal J, Gavioli A, Gossner MM, Granot I, Guarino R, Gustafsson C, Hayden B, He S, Heilmann‐Clausen J, Heino J, Hunter JT, Huszar VLM, Janišová M, Jyrkänkallio‐Mikkola J, Kahilainen KK, Kemppinen J, Kozub Ł, Kruk C, Kulbiki M, Kuzemko A, Christiaan le Roux P, Lehikoinen A, Teixeira de Lima D, Lopez‐Urrutia A, Lukács BA, Luoto M, Mammola S, Marinho MM, Menezes LS, Milardi M, Miranda M, Moser GAO, Mueller J, Niittynen P, Norkko A, Nowak A, Ometto JP, Ovaskainen O, Overbeck GE, Pacheco FS, Pajunen V, Palpurina S, Picazo F, Prieto JAC, Rodil IF, Sabatini FM, Salingré S, De Sanctis M, Segura AM, da Silva LHS, Stevanovic ZD, Swacha G, Teittinen A, Tolonen KT, Tsiripidis I, Virta L, Wang B, Wang J, Weisser W, Xu Y, Soininen J. Distance decay 2.0 - A global synthesis of taxonomic and functional turnover in ecological communities. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2022; 31:1399-1421. [PMID: 35915625 PMCID: PMC9322010 DOI: 10.1111/geb.13513] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 05/05/2023]
Abstract
Aim Understanding the variation in community composition and species abundances (i.e., β-diversity) is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional variation in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distance. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 148 datasets comprising different types of organisms and environments. Location Global. Time period 1990 to present. Major taxa studied From diatoms to mammals. Method We measured the strength of the decay using ranked Mantel tests (Mantel r) and the rate of distance decay as the slope of an exponential fit using generalized linear models. We used null models to test whether functional similarity decays faster or slower than expected given the taxonomic decay along the spatial and environmental distance. We also unveiled the factors driving the rate of decay across the datasets, including latitude, spatial extent, realm and organismal features. Results Taxonomic distance decay was stronger than functional distance decay along both spatial and environmental distance. Functional distance decay was random given the taxonomic distance decay. The rate of taxonomic and functional spatial distance decay was fastest in the datasets from mid-latitudes. Overall, datasets covering larger spatial extents showed a lower rate of decay along spatial distance but a higher rate of decay along environmental distance. Marine ecosystems had the slowest rate of decay along environmental distances. Main conclusions In general, taxonomic distance decay is a useful tool for biogeographical research because it reflects dispersal-related factors in addition to species responses to climatic and environmental variables. Moreover, functional distance decay might be a cost-effective option for investigating community changes in heterogeneous environments.
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Liu Z, Zhou T, Heino J, Castro DMP, Cui Y, Li Z, Wang W, Chen Y, Xie Z. Land conversion induced by urbanization leads to taxonomic and functional homogenization of a river macroinvertebrate metacommunity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153940. [PMID: 35183628 DOI: 10.1016/j.scitotenv.2022.153940] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
Conversion of forests to urban land-use in the processes of urbanization is one of the major causes of biotic homogenization (i.e., decline in beta diversity) in freshwater ecosystems, threating ecosystem functioning and services. However, empirical studies exploring urban land-use shaping patterns of taxonomic and functional beta diversities and their components in subtropical urban rivers are limited. Here, by leveraging data for 43 sampling sites from urban and forest rivers in Shenzhen, a megacity showing rapid urbanization, we determined the spatio-temporal dynamics and associated drivers of taxonomic and functional beta diversities of river macroinvertebrates. Our results showed that, from the forest to urban rivers, taxonomic beta diversity (wet: 32.9%; dry: 17.1%) declined more significantly than functional beta diversity (wet: 17.4%; dry: 9.5%) in different seasons. We further found that these compositional changes were largely driven by decreased roles of species/traits replacement. Although replacement was also dominant for taxonomic beta diversity (60.4%-68.4%) in two sets of rivers, richness difference contributed more to functional beta diversity in the urban river (52.6%-60.5%). Both deterministic and stochastic processes simultaneously affected beta diversity, with stochastic processes being more important in the urban (3.0-19.0%) than forest rivers (0.0%-3.0%). Besides, db-RDA and variation partitioning results showed that local-scale environmental variables explained considerably large fractions of variation in beta diversity. We hence recommended that biodiversity conservation should focus on improving and restoring local environmental conditions. Despite no significant seasonal differences in beta diversity were detected in this study, we found that the roles of deterministic (i.e., local-scale and land-use variables) and stochastic processes varied considerately across seasons. This result highlights the viewpoint that urban river biodiversity monitoring should go beyond one-season snapshot surveys. As the ongoing trend of urbanization in developing countries, the findings of this study are relevant in guiding urban river environmental monitoring, biodiversity conservation and land-use planning.
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Affiliation(s)
- Zhenyuan Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jani Heino
- Freshwater Centre, Finnish Environment Institute, Paavo Havaksen Tie 3, P.O. Box 413, FI-90014 Oulu, Finland
| | - Diego M P Castro
- Department of Genetics, Ecology, and Evolution, Laboratory of Benthos Ecology, Biological Sciences Institute, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Minas Gerais, CEP 31270-901 Belo Horizonte, Brazil
| | - Yongde Cui
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhengfei Li
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weimin Wang
- Central Station for Environmental Monitoring and Assessment, Shenzhen 518049, China
| | - Yushun Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhicai Xie
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Ma S, Fang J, Liu J, Yang X, Lyu T, Wang L, Zhou S, Dou H, Zhang H. Differences in sediment carbon-fixation rate and associated bacterial communities in four wetland types in Hulun Lake Basin. CATENA 2022; 213:106167. [DOI: 10.1016/j.catena.2022.106167] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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38
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Okamoto S, Takenaka M, Tojo K. Seasonal modifications of longitudinal distribution patterns within a stream: Interspecific interactions in the niche overlap zones of two Ephemera mayflies. Ecol Evol 2022; 12:e8766. [PMID: 35386869 PMCID: PMC8975782 DOI: 10.1002/ece3.8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/07/2022] Open
Abstract
Niche differentiation between closely related species leads to differentiation of their habitats. Segregation based on slight differences in environmental factors, that is niche differentiation on the microhabitat scale, allows more species to inhabit a certain geographic space. Therefore, such fine scale niche differentiation is an important factor in the support of species diversity. In addition, niche differentiation on the microhabitat scale and/or the differentiation of breeding seasons can be considered typical mechanisms that facilitate multispecies' co-existence. In this study, sister species (Commonly, Ephemera japonica inhabit at upstream region and Ephemera strigata inhabit at middle stream region), which often coexist in the upper to middle reaches of river systems of the Japanese Islands, were targeted and the following aspects were investigated. First, differences in habitat preference and interspecific differences in flow distribution patterns on a geographically fine scale were tracked in detail. Subsequently, the temporal transitions of their distribution patterns were investigated in detail and seasonal changes were investigated. Finally, we thoroughly investigated the disappearance of nymphs of each species from the river due to emergence affected the distribution of each species (by conducting daily emergence surveys). Combining results of these multiple studies also suggested that there may be spatiotemporal interspecial interaction between these two species within/around their overlapping regions. Traditionally, the longitudinal distribution pattern of these two Ephemera mayflies has been thought to be established based on a difference in habitat preferences, but this study revealed that the interspecific interaction between the two species also plays an important role. This study provides new insights into species diversity and distribution pattern formation in river-dwelling species.
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Affiliation(s)
- Seiya Okamoto
- Division of Mountain and Environmental ScienceInterdisciplinary Graduate School of Science and TechnologyShinshu UniversityMatsumotoJapan
| | - Masaki Takenaka
- Sugadaira Research StationMountain Science CenterUniversity of TsukubaUedaJapan
- Department of BiologyFaculty of ScienceShinshu UniversityMatsumotoJapan
| | - Koji Tojo
- Division of Mountain and Environmental ScienceInterdisciplinary Graduate School of Science and TechnologyShinshu UniversityMatsumotoJapan
- Department of BiologyFaculty of ScienceShinshu UniversityMatsumotoJapan
- Institute of Mountain ScienceShinshu UniversityMatsumotoJapan
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39
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Dong K, Yu Z, Kerfahi D, Lee SS, Li N, Yang T, Adams JM. Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152565. [PMID: 34953844 DOI: 10.1016/j.scitotenv.2021.152565] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/30/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Classically, ecologists have considered that biota becomes more integrated and interdependent with ecosystem development in primary successional environments. However, recent work on soil microbial communities suggests that there may in fact be no change in network integration over successional time series. Here, we performed a test of this principle by identifying network-level topological features of the soil microbial co-occurrence networks in the primary successional foreland environment of the retreating high-Arctic glacier of Midtre Lovénbreen, Svalbard. Soil was sampled at sites along the foreland of inferred ages 10-90 years since deglaciation. DNA was extracted and amplicon sequenced for 16 s rRNA genes for bacteria and ITS1 region for fungi. Despite the chronologically-related soil pH decline and organic C/N accumulation, analysis on network-level topological features showed network integration did not change with inferred chronological ages, whereas network integration declined with decreasing pH and increasing total organic carbon (TOC) - both factors that can be viewed as an indicator of soil development. We also found that bacteria played a greater role in the network structure than fungi, with all keystone species in the microbial co-occurrence network being bacteria species. Both number and relative abundance of the keystone species were significantly higher when soil pH increased or TOC decreased. It appears that in the more extreme and less productive conditions of early primary succession, integration between members of soil biota into consortia may play a greater role in niche adaptation and survival. Our finding also emphasizes that ecosystem development is not simply a product of time but is influenced by locally heterogeneous factors.
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Affiliation(s)
- Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea
| | - Zhi Yu
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, South Korea
| | - Sang-Seob Lee
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Nan Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Nanning, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China.
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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Emery KA, Kramer VR, Schooler NK, Michaud KM, Madden JR, Hubbard DM, Miller RJ, Dugan JE. Habitat partitioning by mobile intertidal invertebrates of sandy beaches shifts with the tides. Ecosphere 2022. [DOI: 10.1002/ecs2.3920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Kyle A. Emery
- Marine Science Institute University of California Santa Barbara California USA
| | - Valerie R. Kramer
- Department of Biology Kent State University at Stark North Canton Ohio USA
| | | | - Kristen M. Michaud
- Marine Science Institute University of California Santa Barbara California USA
| | - Jessica R. Madden
- Marine Science Institute University of California Santa Barbara California USA
| | - David M. Hubbard
- Marine Science Institute University of California Santa Barbara California USA
| | - Robert J. Miller
- Marine Science Institute University of California Santa Barbara California USA
| | - Jenifer E. Dugan
- Marine Science Institute University of California Santa Barbara California USA
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42
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Jiao S, Chen W, Wei G. Core microbiota drive functional stability of soil microbiome in reforestation ecosystems. GLOBAL CHANGE BIOLOGY 2022; 28:1038-1047. [PMID: 34862696 DOI: 10.1111/gcb.16024] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/23/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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43
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Sannassy Pilly S, Richardson LE, Turner JR, Roche RC. Atoll-dependent variation in depth zonation of benthic communities on remote reefs. MARINE ENVIRONMENTAL RESEARCH 2022; 173:105520. [PMID: 34775207 DOI: 10.1016/j.marenvres.2021.105520] [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: 07/02/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The distribution and organisation of benthic organisms on tropical reefs are typically heterogenous yet display distinct zonation patterns across depth gradients. However, there are few datasets which inform our understanding of how depth zonation in benthic community composition varies spatially among and within different reef systems. Here, we assess the depth zonation in benthic forereef slope communities in the Central Indian Ocean, prior to the back-to-back bleaching events in 2014-2017. We compare benthic communities between shallow (5-10 m) and deep (20-25 m) sites, at two spatial scales: among and within 4 atolls. Our analyses showed the variation in both major functional groups and hard coral assemblages between depth varied among atolls, and within-atoll comparisons revealed distinct differences between shallow and deep forereef slope communities. Indicator taxa analyses characterising the hard coral community between depths revealed a higher number of coral genera characteristic of the deep forereef slopes (10) than the shallow forereef slopes (6). Only two coral genera consistently associated with both depths across all atolls, and these were Acropora and Porites. Our results reveal spatial variation in depth zonation of benthic communities, potentially driven by biophysical processes varying across depths and atolls, and provide a baseline to understand and measure the impacts of future global climate change on benthic communities across depths.
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Correa SB, van der Sleen P, Siddiqui SF, Bogotá-Gregory JD, Arantes CC, Barnett AA, Couto TBA, Goulding M, Anderson EP. OUP accepted manuscript. Bioscience 2022; 72:753-768. [PMID: 35923189 PMCID: PMC9343230 DOI: 10.1093/biosci/biac038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Riverine floodplains are biologically diverse and productive ecosystems. Although tropical floodplains remain relatively conserved and ecologically functional compared to those at higher latitudes, they face accelerated hydropower development, climate change, and deforestation. Alterations to the flood pulse could act synergistically with other drivers of change to promote profound ecological state change at a large spatial scale. State change occurs when an ecosystem reaches a critical threshold or tipping point, which leads to an alternative qualitative state for the ecosystem. Visualizing an alternative state for Amazonian floodplains is not straightforward. Yet, it is critical to recognize that changes to the flood pulse could push tropical floodplain ecosystems over a tipping point with cascading adverse effects on biodiversity and ecosystem services. We characterize the Amazonian flood pulse regime, summarize evidence of flood pulse change, assess potential ecological repercussions, and provide a monitoring framework for tracking flood pulse change and detecting biotic responses.
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Affiliation(s)
| | | | | | | | | | | | - Thiago B A Couto
- Florida International University Institute of Environment and a member of the Tropical Rivers Lab
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45
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Tomikawa K, Sasaki T, Aoyagi M, Nakano T. Taxonomy and phylogeny of the genus Melita (Crustacea: Amphipoda: Melitidae) from the West Pacific Islands, with descriptions of four new species. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2021.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Marjakangas E, Muñoz G, Turney S, Albrecht J, Neuschulz EL, Schleuning M, Lessard J. Trait‐based inference of ecological network assembly: a conceptual framework and methodological toolbox. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Emma‐Liina Marjakangas
- Centre for Biodiversity Dynamics, Department of Biology Norwegian University of Science and Technology Trondheim Norway
- Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Gabriel Muñoz
- Department of Biology, Faculty of Arts and Sciences Concordia University, 7141 Sherbrooke Street West, Montreal Quebec Canada
| | - Shaun Turney
- Department of Biology, Faculty of Arts and Sciences Concordia University, 7141 Sherbrooke Street West, Montreal Quebec Canada
| | - Jörg Albrecht
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F), Senckenberganlage 25 Frankfurt am Main Germany
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F), Senckenberganlage 25 Frankfurt am Main Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F), Senckenberganlage 25 Frankfurt am Main Germany
| | - Jean‐Philippe Lessard
- Department of Biology, Faculty of Arts and Sciences Concordia University, 7141 Sherbrooke Street West, Montreal Quebec Canada
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47
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Torralvo K, Fraga R, Lima AP, Dayrell J, Magnusson WE. Environmental filtering and deforestation shape frog assemblages in Amazonia: An empirical approach assessing species abundances and functional traits. Biotropica 2021. [DOI: 10.1111/btp.13053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Kelly Torralvo
- Programa de Pós‐Graduação em Ecologia Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Rafael Fraga
- Laboratório de Ecologia e Comportamento Animal Universidade Federal do Oeste do Pará Santarém Brazil
| | - Albertina P. Lima
- Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Jussara Dayrell
- Programa de Pós‐Graduação em Ecologia Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - William E. Magnusson
- Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
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Zahid MS, Li D, Javed HU, Sabir IA, Wang L, Jiu S, Song S, Ma C, Wang D, Zhang C, Zhou X, Xu W, Wang S. Comparative fungal diversity and dynamics in plant compartments at different developmental stages under root-zone restricted grapevines. BMC Microbiol 2021; 21:317. [PMID: 34784893 PMCID: PMC8594160 DOI: 10.1186/s12866-021-02376-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The root-zone restriction cultivation technique is used to achieve superior fruit quality at the cost of limited vegetative and enhanced reproductive development of grapevines. Fungal interactions and diversity in grapevines are well established; however, our knowledge about fungal diversity under the root-zone restriction technique is still unexplored. To provide insights into the role of mycobiota in the regulation of growth and fruit quality of grapevine under root-zone restriction, DNA from rhizosphere and plant compartments, including white roots (new roots), leaves, flowers, and berries of root-zone restricted (treatment) and conventionally grown plants (control), was extracted at three growth stages (full bloom, veraison, and maturity). RESULTS Diversity analysis based on the ITS1 region was performed using QIIME2. We observed that the root-zone restriction technique primarily affected the fungal communities of the soil and plant compartments at different growth stages. Interestingly, Fusarium, Ilyonectria, Cladosporium and Aspergillus spp observed in the rhizosphere overlapped with the phyllosphere at all phenological stages, having distinctive abundance in grapevine habitats. Peak richness and diversity were observed in the rhizosphere at the full bloom stage of control plants, white roots at the veraison stage of treatment, leaves at the maturity stage of treatment, flowers at the full bloom stage and berries at the veraison stage of control plants. Except for white roots, the diversity of soil and plant compartments of treated plants tended to increase until maturity. At the maturity stage of the treated and control plants, the abundance of Aspergillus spp. was 25.99 and 29.48%, respectively. Moreover, the total soluble sugar content of berries was 19.03 obrix and 16 obrix in treated and control plants, respectively, at the maturity stage. CONCLUSIONS This is the first elucidative study targeting the fungal diversity of conventional and root-restricted cultivation techniques in a single vineyard. Species richness and diversity are affected by stressful cultivation known as root zone restriction. There is an association between the abundance of Aspergillus spp. and fruit quality because despite causing stress to the grapevine, superior quality of fruit is retrieved in root-zone restricted plants.
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Affiliation(s)
- Muhammad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dongmei Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hafiz Umer Javed
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dapeng Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xuhui Zhou
- Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241 China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
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Examining the generality of the biphasic transition from niche-structured to immigration-structured communities. THEOR ECOL-NETH 2021. [DOI: 10.1007/s12080-021-00521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Carvalho ASR, de Andrade LG, de Andrade ACS. Germination of small tropical seeds has distinct light quality and temperature requirements, depending on microhabitat. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:981-991. [PMID: 34532932 DOI: 10.1111/plb.13328] [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: 05/02/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The coexistence of plant species in tropical rainforests is related to specific abiotic resources, varying according to the occurrence microhabitat of each species. Light quality is the main abiotic factor influencing germination of small seeds; however, studies often do not discriminate its effect from that of light irradiance. This study compared specific requirements for seed germination of ten small-seeded species, with restricted occurrence in only one of three contrasting microhabitats: forest understorey, edge of clearings and open areas. Laboratory experiments were carried out to test temperature regime (constant or fluctuating), light quality (R:FR) and light irradiance (PAR), which reproduce high and low conditions commonly found in the microhabitats. Seed germination of all species occurred between 20 and 30 °C, only seeds of open area species were able to germinate at 35 °C and no species required alternating temperatures to germinate. Irrespective of species and microhabitat, a decrease in the R:FR reduced the germination percentage; however, there were differences in the capacity to germinate at low R:FR. The values of R:FR50% were higher for open area and edge species (0.441-0.345) than for understorey species (0.181-0.109), with few exceptions. For all species and most of the tests, germination was not influenced by PAR. Light quality is the most important light signal for germination of small seeds; irradiance has little effect. Our results suggest two distinct patterns of germination for small-seeded species: open area and edge species are light-demanding and require high R:FR to germinate, while understorey species are shade-tolerant and germinate at low R:FR. These differences are responsible for distinct microhabitat occurrence and help to explain the coexistence of species in tropical forests.
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Affiliation(s)
- A S R Carvalho
- Seed Laboratory, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - L G de Andrade
- Seed Laboratory, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Programa de Pós-graduação em Biologia Vegetal - IBRAG - Universidade do Estado do Rio de Janeiro, Janeiro, RJ, Brazil
| | - A C S de Andrade
- Seed Laboratory, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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