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Li Q, Cheng X, Liu X, Gao P, Wang H, Su C, Huang Q. Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts. Front Microbiol 2024; 15:1377721. [PMID: 38659982 PMCID: PMC11041041 DOI: 10.3389/fmicb.2024.1377721] [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: 01/28/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.
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Affiliation(s)
- Qing Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Pengfei Gao
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Chuntian Su
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo, Guangxi, China
| | - Qibo Huang
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo, Guangxi, China
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Noguerales V, Meramveliotakis E, Castro-Insua A, Andújar C, Arribas P, Creedy TJ, Overcast I, Morlon H, Emerson BC, Vogler AP, Papadopoulou A. Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests. Mol Ecol 2023; 32:6110-6128. [PMID: 34775647 DOI: 10.1111/mec.16275] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 01/04/2023]
Abstract
Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.
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Affiliation(s)
- Víctor Noguerales
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | | | | | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de La Laguna, Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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Perry KI, Sivakoff FS, Wallin KF, Wenzel JW, Herms DA. Forest disturbance and arthropods: small‐scale canopy and understory disturbances alter movement of mobile arthropods. Ecosphere 2021. [DOI: 10.1002/ecs2.3771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Kayla I. Perry
- Department of Entomology The Ohio State University 1680 Madison Avenue Wooster Ohio 44691 USA
| | - Frances S. Sivakoff
- Department of Evolution, Ecology, and Organismal Biology The Ohio State University 1465 Mount Vernon Avenue Marion Ohio 43302 USA
| | - Kimberly F. Wallin
- Rubenstein School of Environment and Natural Resources University of Vermont Aiken Center Burlington Vermont 05405 USA
- USDA Forest Service Northern Research Station Aiken Burlington Vermont 05405 USA
| | - John W. Wenzel
- Powdermill Nature Reserve Carnegie Museum of Natural History 1795 Route 381 Rector Pennsylvania 15677 USA
| | - Daniel A. Herms
- Department of Entomology The Ohio State University 1680 Madison Avenue Wooster Ohio 44691 USA
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Ground-Dwelling Arthropod Community Responses to Recent and Repeated Wildfires in Conifer Forests of Northern New Mexico, USA. FORESTS 2019. [DOI: 10.3390/f10080667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The increasing frequency and severity of wildfires in semi-arid conifer forests as a result of global change pressures has raised concern over potential impacts on biodiversity. Ground-dwelling arthropod communities represent a substantial portion of diversity in conifer forests, and could be particularly impacted by wildfires. In addition to direct mortality, wildfires can affect ground-dwelling arthropods by altering understory characteristics and associated deterministic community assembly processes (e.g., environmental sorting). Alternatively, disturbances have been reported to increase the importance of stochastic community assembly processes (e.g., probabilistic dispersal and colonization rates). Utilizing pitfall traps to capture ground-dwelling arthropods within forest stands that were burned by one or two wildfires since 1996 in the Jemez Mountains of northern New Mexico, United States (USA), we examined the potential influences of deterministic versus stochastic processes on the assembly of these diverse understory communities. Based on family-level and genera-level arthropod identifications, we found that the multivariate community structures differed among the four fire groups surveyed, and were significantly influenced by the quantities of duff, litter, and coarse woody debris, in addition to tree basal area and graminoid cover. Taxon diversity was positively related to duff quantities, while taxon turnover was positively linked to exposed-rock cover and the number of logs on the ground. Despite the significant effects of these understory properties on the arthropod community structure, a combination of null modeling and metacommunity analysis revealed that both deterministic and stochastic processes shape the ground-dwelling arthropod communities in this system. However, the relative influence of these processes as a function of time since the wildfires or the number of recent wildfires was not generalizable across the fire groups. Given that different assembly processes shaped arthropod communities among locations that had experienced similar disturbances over time, increased efforts to understand the processes governing arthropod community assembly following disturbance is required in this wildfire-prone landscape.
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Mlynarek JJ, Grégoire Taillefer A, Wheeler TA. Saproxylic Diptera assemblages in a temperate deciduous forest: implications for community assembly. PeerJ 2018; 6:e6027. [PMID: 30533313 PMCID: PMC6284445 DOI: 10.7717/peerj.6027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/29/2018] [Indexed: 12/04/2022] Open
Abstract
Saproxylic insects, those associated directly or indirectly with decaying wood for all or part of their life cycle, compose a large proportion of forest organisms. Flies (Diptera) are often the most abundant and species-rich group of insects in forest microhabitats, yet most work to date on saproxylic insect diversity and ecology has focused on beetles (Coleoptera). We compared saproxylic Diptera assemblages reared from two tree species (sugar maple and American beech) at two stages of decay (early/young and advanced/old) for a total of 20 logs in an eastern Canadian Nearctic old-growth forest. We found that communities are distinct within both species type and decay stage of wood. Early decay stage wood is more variable in community composition than later decay stage; however, as the age of the decaying wood increases, the abundance of Diptera increases significantly. Most indicator species are discernible in later decay stage and wood type. We venture to suggest that stochastic and deterministic processes may play a role in driving Diptera communities in temperate deciduous forests. To retain the highest saproxylic Diptera diversity in a forest, a variety of decaying wood types at different stages of decomposition is necessary.
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Affiliation(s)
- Julia J Mlynarek
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada.,Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Amélie Grégoire Taillefer
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada.,BioÉco Environnement, Pincourt, QC, Canada
| | - Terry A Wheeler
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
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Dong X, Lytle DA, Olden JD, Schriever TA, Muneepeerakul R. Importance of neutral processes varies in time and space: Evidence from dryland stream ecosystems. PLoS One 2017; 12:e0176949. [PMID: 28486499 PMCID: PMC5423606 DOI: 10.1371/journal.pone.0176949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/19/2017] [Indexed: 11/18/2022] Open
Abstract
Many ecosystems experience strong temporal variability in environmental conditions; yet, a clear picture of how niche and neutral processes operate to determine community assembly in temporally variable systems remains elusive. In this study, we constructed neutral metacommunity models to assess the relative importance of neutral processes in a spatially and temporally variable ecosystem. We analyzed macroinvertebrate community data spanning multiple seasons and years from 20 sites in a Sonoran Desert river network in Arizona. The model goodness-of-fit was used to infer the importance of neutral processes. Averaging over eight stream flow conditions across three years, we found that neutral processes were more important in perennial streams than in non-perennial streams (intermittent and ephemeral streams). Averaging across perennial and non-perennial streams, we found that neutral processes were more important during very high flow and in low flow periods; whereas, at very low flows, the relative importance of neutral processes varied greatly. These findings were robust to the choice of model parameter values. Our study suggested that the net effect of disturbance on the relative importance of niche and neutral processes in community assembly varies non-monotonically with the severity of disturbance. In contrast to the prevailing view that disturbance promotes niche processes, we found that neutral processes could become more important when the severity of disturbance is beyond a certain threshold such that all organisms are adversely affected regardless of their biological traits and strategies.
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Affiliation(s)
- Xiaoli Dong
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Nicholas School of the Environment, Duke University, Durham, North Carolina, United States of America
| | - David A. Lytle
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Julian D. Olden
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Tiffany A. Schriever
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, United States of America
- Institute of the Environment& Sustainability, Western Michigan University, Kalamazoo, Michigan, United States of America
| | - Rachata Muneepeerakul
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, United States of America
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