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Rui J, Zhao Y, Cong N, Wang F, Li C, Liu X, Hu J, Ling N, Jing X. Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities. Front Microbiol 2023; 14:1280011. [PMID: 37808282 PMCID: PMC10557256 DOI: 10.3389/fmicb.2023.1280011] [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: 08/19/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.
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Affiliation(s)
- Junpeng Rui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuwei Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Nan Cong
- Lhasa Plateau Ecosystem Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Fuxin Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Chao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jingjing Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ning Ling
- Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xin Jing
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Schnecker J, Spiegel F, Li Y, Richter A, Sandén T, Spiegel H, Zechmeister-Boltenstern S, Fuchslueger L. Microbial responses to soil cooling might explain increases in microbial biomass in winter. BIOGEOCHEMISTRY 2023; 164:521-535. [PMID: 37475883 PMCID: PMC10354169 DOI: 10.1007/s10533-023-01050-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/15/2023] [Indexed: 07/22/2023]
Abstract
In temperate, boreal and arctic soil systems, microbial biomass often increases during winter and decreases again in spring. This build-up and release of microbial carbon could potentially lead to a stabilization of soil carbon during winter times. Whether this increase is caused by changes in microbial physiology, in community composition, or by changed substrate allocation within microbes or communities is unclear. In a laboratory incubation study, we looked into microbial respiration and growth, as well as microbial glucose uptake and carbon resource partitioning in response to cooling. Soils taken from a temperate beech forest and temperate cropland system in October 2020, were cooled down from field temperature of 11 °C to 1 °C. We determined microbial growth using 18O-incorporation into DNA after the first two days of cooling and after an acclimation phase of 9 days; in addition, we traced 13C-labelled glucose into microbial biomass, CO2 respired from the soil, and into microbial phospholipid fatty acids (PLFAs). Our results show that the studied soil microbial communities responded strongly to soil cooling. The 18O data showed that growth and cell division were reduced when soils were cooled from 11 to 1 °C. Total respiration was also reduced but glucose uptake and glucose-derived respiration were unchanged. We found that microbes increased the investment of glucose-derived carbon in unsaturated phospholipid fatty acids at colder temperatures. Since unsaturated fatty acids retain fluidity at lower temperatures compared to saturated fatty acids, this could be interpreted as a precaution to reduced temperatures. Together with the maintained glucose uptake and reduced cell division, our findings show an immediate response of soil microorganisms to soil cooling, potentially to prepare for freezing events. The discrepancy between C uptake and cell division could explain previously observed high microbial biomass carbon in temperate soils in winter. Supplementary Information The online version contains supplementary material available at 10.1007/s10533-023-01050-x.
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Affiliation(s)
- Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Felix Spiegel
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Yue Li
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Taru Sandén
- Department for Soil Health and Plant Nutrition, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Heide Spiegel
- Department for Soil Health and Plant Nutrition, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | | | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Zhao W, Wang DD, Huang KC, Liu S, Reyila M, Sun YF, Li JN, Cui BK. Seasonal variation in the soil fungal community structure of Larix gmelinii forests in Northeast China. Front Microbiol 2023; 14:1106888. [PMID: 37032849 PMCID: PMC10073431 DOI: 10.3389/fmicb.2023.1106888] [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: 11/24/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Soil fungi play an indispensable role in forest ecosystems by participating in energy flow, material circulation, and assisting plant growth and development. Larix gmelinii is the dominant tree species in the greater Khingan Mountains, which is the only cold temperate coniferous forest in China. Understanding the variations in underground fungi will help us master the situation of L. gmelinii above ground. We collected soil samples from three seasons and analyzed the differences in soil fungal community structure using high-throughput sequencing technology to study the seasonal changes in soil fungal community structure in L. gmelinii forests. We found that the Shannon and Chao1 diversity in autumn was significantly lower than in spring and summer. The community composition and functional guild varied significantly between seasons. Furthermore, we showed that ectomycorrhizal fungi dominated the functional guilds. The relative abundance of ectomycorrhizal fungi increased dramatically from summer to autumn and was significantly negatively correlated with temperature and precipitation. Temperature and precipitation positively affect the alpha diversity of fungi significantly. In addition, pH was negatively correlated with the Chao1 diversity. Temperature and precipitation significantly affected several dominant genera and functional guilds. Among the soil physicochemical properties, several dominant genera were affected by pH, and the remaining individual genera and functional guilds were significantly correlated with total nitrogen, available phosphorus, soil organic carbon, or cation exchange capacity. For the composition of total fungal community, temperature and precipitation, as well as soil physicochemical properties except AP, significantly drove the variation in community composition.
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Poppeliers SWM, Hefting M, Dorrepaal E, Weedon JT. Functional microbial ecology in arctic soils: the need for a year-round perspective. FEMS Microbiol Ecol 2022; 98:6824434. [PMID: 36368693 PMCID: PMC9701097 DOI: 10.1093/femsec/fiac134] [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: 03/31/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial ecology of arctic and sub-arctic soils is an important aspect of the global carbon cycle, due to the sensitivity of the large soil carbon stocks to ongoing climate warming. These regions are characterized by strong climatic seasonality, but the emphasis of most studies on the short vegetation growing season could potentially limit our ability to predict year-round ecosystem functions. We compiled a database of studies from arctic, subarctic, and boreal environments that include sampling of microbial community and functions outside the growing season. We found that for studies comparing across seasons, in most environments, microbial biomass and community composition vary intra-annually, with the spring thaw period often identified by researchers as the most dynamic time of year. This seasonality of microbial communities will have consequences for predictions of ecosystem function under climate change if it results in: seasonality in process kinetics of microbe-mediated functions; intra-annual variation in the importance of different (a)biotic drivers; and/or potential temporal asynchrony between climate change-related perturbations and their corresponding effects. Future research should focus on (i) sampling throughout the entire year; (ii) linking these multi-season measures of microbial community composition with corresponding functional or physiological measurements to elucidate the temporal dynamics of the links between them; and (iii) identifying dominant biotic and abiotic drivers of intra-annual variation in different ecological contexts.
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Affiliation(s)
- Sanne W M Poppeliers
- Corresponding author: Department of Biology, Utrecht University, 3584 CH, The Netherlands. E-mail:
| | - Mariet Hefting
- Department of Biology, Utrecht University, 3584 CH, The Netherlands
| | - Ellen Dorrepaal
- Climate Impacts Research Centre, Umea University, SE-981 07, Abisko, Sweden
| | - James T Weedon
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
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Factors Affecting the Natural Regeneration of the Larix principis-rupprechtii Mayr Plantations: Evidence from the Composition and Co-Occurrence Network Structure of Soil Bacterial Communities. Processes (Basel) 2022. [DOI: 10.3390/pr10091771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bacterial communities living in the soil can affect forests natural regeneration, but the effects of their composition and network inference on regeneration of Larix principis-rupprechtii Mayr plantations remain largely elusive. Therefore, the redundancy analysis and structure equations modeling of affecting elements for the regeneration of L. principis-rupprechtii plots including the diversity, composition and network structure of soil bacteria, topographic factors, light factors, and soil physicochemical properties have been conducted. It was found that the increased modularity of the soil bacterial community co-occurrence network and the enrichment of metabolic pathway bacteria had a significant positive effect on the successful regeneration (total effect of 0.84). The complexity of the soil bacterial community gradually decreased with the increase of stand regeneration, and the composition and structure of the flora became simpler (with standard path coefficients: −0.70). In addition, altitude also had a positive effect on regeneration with a total effect of 0.39. Soil nutrients had significantly negative effects on regeneration with total effects of −0.87. Soil bacterial communities may mediate the effects of soil nutrients, altitude, litter thickness, and herbaceous diversity on regeneration in L. principis-rupprechtii plantations. The results provide a great contribution to our understanding of regeneration-soil bacterial community interactions and the basis and important data for sustainable management of L. principis-rupprechtii plantations in the Lvliang Mountains located in northern China.
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Zhang J, Ma A, Zhou H, Chen X, Zhou X, Liu G, Zhuang X, Qin X, Priemé A, Zhuang G. Unexpected high carbon losses in a continental glacier foreland on the Tibetan Plateau. ISME COMMUNICATIONS 2022; 2:68. [PMID: 37938688 PMCID: PMC9723710 DOI: 10.1038/s43705-022-00148-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/19/2022] [Accepted: 06/28/2022] [Indexed: 10/21/2023]
Abstract
Closely related with microbial activities, soil developments along the glacier forelands are generally considered a carbon sink; however, those of continental glacier forelands remain unclear. Continental glaciers are characterized by dry conditions and low temperature that limit microbial growth. We investigated the carbon characteristics along a chronosequence of the Laohugou Glacier No. 12 foreland, a typical continental glacier on the Tibetan Plateau, by analyzing soil bacterial community structure and microbial carbon-related functional potentials. We found an unexpected carbon loss in which soil organic carbon decreased from 22.21 g kg-1 to 10.77 g kg-1 after receding 50 years. Structural equation modeling verified the important positive impacts from bacterial community. Lower carbon fixation efficiency along the chronosequence was supported by less autotrophic bacteria and carbon fixation genes relating to the reductive tricarboxylic acid cycle. Lower carbon availability and higher carbon requirements were identified by an increasing bacterial copy number and a shift of the dominant bacterial community from Proteobacteria and Bacteroidetes (r-strategists) to Actinobacteria and Acidobacteria (K-strategists). Our findings show that the carbon loss of continental glacier foreland was significantly affected by the changes of bacterial community, and can help to avoid overestimating the carbon sink characteristics of glacier forelands in climate models.
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Affiliation(s)
- Jiejie Zhang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101400, China
- Sino-Danish Center for Education and Research, Beijing, 101400, China
| | - Anzhou Ma
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hanchang Zhou
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianke Chen
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101400, China
- Sino-Danish Center for Education and Research, Beijing, 101400, China
| | - Xiaorong Zhou
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guohua Liu
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiang Qin
- Qilian Shan Station of Glaciology and Eco-environment, State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Anders Priemé
- Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Center for Permafrost, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Guoqiang Zhuang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Chen J, Shi Z, Liu S, Zhang M, Cao X, Chen M, Xu G, Xing H, Li F, Feng Q. Altitudinal Variation Influences Soil Fungal Community Composition and Diversity in Alpine–Gorge Region on the Eastern Qinghai–Tibetan Plateau. J Fungi (Basel) 2022; 8:jof8080807. [PMID: 36012795 PMCID: PMC9410234 DOI: 10.3390/jof8080807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/04/2022] Open
Abstract
Soil fungi play an integral and essential role in maintaining soil ecosystem functions. The understanding of altitude variations and their drivers of soil fungal community composition and diversity remains relatively unclear. Mountains provide an open, natural platform for studying how the soil fungal community responds to climatic variability at a short altitude distance. Using the Illumina MiSeq high-throughput sequencing technique, we examined soil fungal community composition and diversity among seven vegetation types (dry valley shrub, valley-mountain ecotone broadleaved mixed forest, subalpine broadleaved mixed forest, subalpine coniferous-broadleaved mixed forest, subalpine coniferous forest, alpine shrub meadow, alpine meadow) along a 2582 m altitude gradient in the alpine–gorge region on the eastern Qinghai–Tibetan Plateau. Ascomycota (47.72%), Basidiomycota (36.58%), and Mortierellomycota (12.14%) were the top three soil fungal dominant phyla in all samples. Soil fungal community composition differed significantly among the seven vegetation types along altitude gradients. The α-diversity of soil total fungi and symbiotic fungi had a distinct hollow pattern, while saprophytic fungi and pathogenic fungi showed no obvious pattern along altitude gradients. The β-diversity of soil total fungi, symbiotic fungi, saprophytic fungi, and pathogenic fungi was derived mainly from species turnover processes and exhibited a significant altitude distance-decay pattern. Soil properties explained 31.27−34.91% of variation in soil fungal (total and trophic modes) community composition along altitude gradients, and the effects of soil nutrients on fungal community composition varied by trophic modes. Soil pH was the main factor affecting α-diversity of soil fungi along altitude gradients. The β-diversity and turnover components of soil total fungi and saprophytic fungi were affected by soil properties and geographic distance, while those of symbiotic fungi and pathogenic fungi were affected only by soil properties. This study deepens our knowledge regarding altitude variations and their drivers of soil fungal community composition and diversity, and confirms that the effects of soil properties on soil fungal community composition and diversity vary by trophic modes along altitude gradients in the alpine–gorge region.
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Affiliation(s)
- Jian Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Zuomin Shi
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
- Correspondence:
| | - Shun Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Miaomiao Zhang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Xiangwen Cao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Miao Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Gexi Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Hongshuang Xing
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Feifan Li
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Qiuhong Feng
- Ecological Restoration and Conservation on Forest and Wetland Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu 610081, China;
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Winkel M, Trivedi CB, Mourot R, Bradley JA, Vieth-Hillebrand A, Benning LG. Seasonality of Glacial Snow and Ice Microbial Communities. Front Microbiol 2022; 13:876848. [PMID: 35651494 PMCID: PMC9149292 DOI: 10.3389/fmicb.2022.876848] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/26/2022] [Indexed: 01/03/2023] Open
Abstract
Blooms of microalgae on glaciers and ice sheets are amplifying surface ice melting rates, which are already affected by climate change. Most studies on glacial microorganisms (including snow and glacier ice algae) have so far focused on the spring and summer melt season, leading to a temporal bias, and a knowledge gap in our understanding of the variations in microbial diversity, productivity, and physiology on glacier surfaces year-round. Here, we investigated the microbial communities from Icelandic glacier surface snow and bare ice habitats, with sampling spanning two consecutive years and carried out in both winter and two summer seasons. We evaluated the seasonal differences in microbial community composition using Illumina sequencing of the 16S rRNA, 18S rRNA, and ITS marker genes and correlating them with geochemical signals in the snow and ice. During summer, Chloromonas, Chlainomonas, Raphidonema, and Hydrurus dominated surface snow algal communities, while Ancylonema and Mesotaenium dominated the surface bare ice habitats. In winter, algae could not be detected, and the community composition was dominated by bacteria and fungi. The dominant bacterial taxa found in both winter and summer samples were Bacteriodetes, Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria. The winter bacterial communities showed high similarities to airborne and fresh snow bacteria reported in other studies. This points toward the importance of dry and wet deposition as a wintertime source of microorganisms to the glacier surface. Winter samples were also richer in nutrients than summer samples, except for dissolved organic carbon-which was highest in summer snow and ice samples with blooming microalgae, suggesting that nutrients are accumulated during winter but primarily used by the microbial communities in the summer. Overall, our study shows that glacial snow and ice microbial communities are highly variable on a seasonal basis.
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Affiliation(s)
- Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre for Geosciences, Potsdam, Germany
| | - Christopher B Trivedi
- GFZ German Research Centre for Geosciences, Helmholtz Centre for Geosciences, Potsdam, Germany
| | - Rey Mourot
- GFZ German Research Centre for Geosciences, Helmholtz Centre for Geosciences, Potsdam, Germany
| | - James A Bradley
- GFZ German Research Centre for Geosciences, Helmholtz Centre for Geosciences, Potsdam, Germany.,School of Geography, Queen Mary University of London, London, United Kingdom
| | - Andrea Vieth-Hillebrand
- GFZ German Research Centre for Geosciences, Helmholtz Centre for Geosciences, Potsdam, Germany
| | - Liane G Benning
- GFZ German Research Centre for Geosciences, Helmholtz Centre for Geosciences, Potsdam, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
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9
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Hariharan J, Buckley DH. Elevational Gradients Impose Dispersal Limitation on Streptomyces. Front Microbiol 2022; 13:856263. [PMID: 35592003 PMCID: PMC9113539 DOI: 10.3389/fmicb.2022.856263] [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: 01/17/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Dispersal governs microbial biogeography, but the rates and mechanisms of dispersal remain poorly characterized for most microbial taxa. Dispersal limitation is driven by limits on dissemination and establishment, respectively. Elevation gradients create striking patterns of biogeography because they produce steep environmental gradients at small spatial scales, and these gradients offer a powerful tool to examine mechanisms of dispersal limitation. We focus on Streptomyces, a bacterial genus common to soil, by using a taxon-specific phylogenetic marker, the RNA polymerase-encoding rpoB gene. By targeting Streptomyces, we assess dispersal limitation at finer phylogenetic resolution than is possible using whole community analyses. We characterized Streptomyces diversity at local spatial scales (100 to 3,000 m) in two temperate forest sites located in the Adirondacks region of New York State: Woods Lake (<100 m elevation change), and Whiteface Mountain (>1,000 m elevation change). Beta diversity varied considerably at both locations, indicative of dispersal limitation acting at local spatial scales, but beta diversity was significantly higher at Whiteface Mountain. Beta diversity varied across elevation at Whiteface Mountain, being lowest at the mountain’s base. We show that Streptomyces taxa exhibit elevational preferences, and these preferences are phylogenetically conserved. These results indicate that habitat preferences influence Streptomyces biogeography and suggest that barriers to establishment structure Streptomyces communities at higher elevations. These data illustrate that Streptomyces biogeography is governed by dispersal limitation resulting from a complex mixture of stochastic and deterministic processes.
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Affiliation(s)
- Janani Hariharan
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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10
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Azorella Cushion Plants and Aridity are Important Drivers of Soil Microbial Communities in Andean Ecosystems. Ecosystems 2021. [DOI: 10.1007/s10021-021-00603-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Liu B, Qu Z, Ma Y, Xu J, Chen P, Sun H. Eucalyptus Plantation Age and Species Govern Soil Fungal Community Structure and Function Under a Tropical Monsoon Climate in China. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:703467. [PMID: 37744134 PMCID: PMC10512287 DOI: 10.3389/ffunb.2021.703467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/17/2021] [Indexed: 09/26/2023]
Abstract
Fungi perform crucial roles in nutrient cycles, but there is limited information on how soil fungal communities vary with stand age and tree species. Eucalyptus has been extensively planted in China, which has caused severe soil erosion and water deficiency due to short rotation management. In this study, the fungal community structure and potential function in Eucalyptus plantations with different ages (1-5+ years) and species (Eucalyptus urophylla × Eucalyptus grandis, Eucalyptus camaldulens, and Eucalyptus pellita) under a tropical monsoon climate in China were characterized by Illumina Miseq coupled with FUNGuild analysis. The results showed that the fungal alpha diversity decreased with an increase in the age of the plantation. Plantations of different ages and species formed distinct fungal communities and potential functional structures, respectively (p < 0.05), in which the age of the plantation contributed more to the variations. At high taxonomic levels, the soil fungal community changed from the dominance of orders belonging to Ascomycota (Pleosporales, Chaetothyriales, and Eurotiales) to orders belonging to Basidiomycota (Agaricales, Sebacinales, Cantharellales, and Russulales) with increasing plantation age. The community potential function shifted from the dominance of plant pathogens to a higher abundance of saprotrophs and symbiotrophs. The organic carbon of the soil was the key environmental driver to both the fungal community and potential functional structure. The results provide useful information on the importance of fungi for the management of Eucalyptus plantations.
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Affiliation(s)
- Bing Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaolei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yang Ma
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jie Xu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Pei Chen
- Department of Applied Foreign Languages, College of Continuing Education, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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12
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Collins CG, Spasojevic MJ, Alados CL, Aronson EL, Benavides JC, Cannone N, Caviezel C, Grau O, Guo H, Kudo G, Kuhn NJ, Müllerová J, Phillips ML, Pombubpa N, Reverchon F, Shulman HB, Stajich JE, Stokes A, Weber SE, Diez JM. Belowground impacts of alpine woody encroachment are determined by plant traits, local climate, and soil conditions. GLOBAL CHANGE BIOLOGY 2020; 26:7112-7127. [PMID: 32902066 DOI: 10.1111/gcb.15340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 08/26/2020] [Indexed: 05/17/2023]
Abstract
Global climate and land use change are causing woody plant encroachment in arctic, alpine, and arid/semi-arid ecosystems around the world, yet our understanding of the belowground impacts of this phenomenon is limited. We conducted a globally distributed field study of 13 alpine sites across four continents undergoing woody plant encroachment and sampled soils from both woody encroached and nearby herbaceous plant community types. We found that woody plant encroachment influenced soil microbial richness and community composition across sites based on multiple factors including woody plant traits, site level climate, and abiotic soil conditions. In particular, root symbiont type was a key determinant of belowground effects, as Nitrogen-fixing woody plants had higher soil fungal richness, while Ecto/Ericoid mycorrhizal species had higher soil bacterial richness and symbiont types had distinct soil microbial community composition. Woody plant leaf traits indirectly influenced soil microbes through their impact on soil abiotic conditions, primarily soil pH and C:N ratios. Finally, site-level climate affected the overall magnitude and direction of woody plant influence, as soil fungal and bacterial richness were either higher or lower in woody encroached versus herbaceous soils depending on mean annual temperature and precipitation. All together, these results document global impacts of woody plant encroachment on soil microbial communities, but highlight that multiple biotic and abiotic pathways must be considered to scale up globally from site- and species-level patterns. Considering both the aboveground and belowground effects of woody encroachment will be critical to predict future changes in alpine ecosystem structure and function and subsequent feedbacks to the global climate system.
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Affiliation(s)
- Courtney G Collins
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Marko J Spasojevic
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Emma L Aronson
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | | | | | - Chatrina Caviezel
- Department of Environmental Sciences, Physical Geography and Environmental Change, University of Basel, Basel, Switzerland
| | - Oriol Grau
- Global Ecology Unit, Campus de Bellaterra (UAB), CREAF, Barcelona, Spain
- Cirad, UMR EcoFoG (AgroParisTech, CNRS, Inra, Univ Antilles, Univ Guyane), Kourou, French Guiana
| | - Hui Guo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Gaku Kudo
- Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Nikolas J Kuhn
- Department of Environmental Sciences, Physical Geography and Environmental Change, University of Basel, Basel, Switzerland
| | - Jana Müllerová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Michala L Phillips
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- US Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología (INECOL), Pátzcuaro, Mexico
| | - Hannah B Shulman
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Alexia Stokes
- University Montpellier, AMAP, INRAE, CIRAD, IRD, CNRS, Montpellier, France
| | - Sören E Weber
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
- Institut für Evolutionsbiologie und Umweltwissenschaften, Universität Zürich, Zürich, Switzerland
| | - Jeffrey M Diez
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
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13
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Karageorgiou C, Tarrío R, Rodríguez-Trelles F. The Cyclically Seasonal Drosophila subobscura Inversion O 7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. Front Genet 2020; 11:565836. [PMID: 33193649 PMCID: PMC7584159 DOI: 10.3389/fgene.2020.565836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/28/2022] Open
Abstract
Chromosome inversions are important contributors to standing genetic variation in Drosophila subobscura. Presently, the species is experiencing a rapid replacement of high-latitude by low-latitude inversions associated with global warming. Yet not all low-latitude inversions are correlated with the ongoing warming trend. This is particularly unexpected in the case of O7 because it shows a regular seasonal cycle that peaks in summer and rose with a heatwave. The inconsistent behavior of O7 across components of the ambient temperature suggests that is causally more complex than simply due to temperature alone. In order to understand the dynamics of O7, high-quality genomic data are needed to determine both the breakpoints and the genetic content. To fill this gap, here we generated a PacBio long read-based chromosome-scale genome assembly, from a highly homozygous line made isogenic for an O3 + 4 + 7 chromosome. Then we isolated the complete continuous sequence of O7 by conserved synteny analysis with the available reference genome. Main findings include the following: (i) the assembled O7 inversion stretches 9.936 Mb, containing > 1,000 annotated genes; (ii) O7 had a complex origin, involving multiple breaks associated with non-B DNA-forming motifs, formation of a microinversion, and ectopic repair in trans with the two homologous chromosomes; (iii) the O7 breakpoints carry a pre-inversion record of fragility, including a sequence insertion, and transposition with later inverted duplication of an Attacin immunity gene; and (iv) the O7 inversion relocated the major insulin signaling forkhead box subgroup O (foxo) gene in tight linkage with its antagonistic regulatory partner serine/threonine-protein kinase B (Akt1) and disrupted concerted evolution of the two inverted Attacin duplicates, reattaching them to dFOXO metabolic enhancers. Our findings suggest that O7 exerts antagonistic pleiotropic effects on reproduction and immunity, setting a framework to understand its relationship with climate change. Furthermore, they are relevant for fragility in genome rearrangement evolution and for current views on the contribution of breakage versus repair in shaping inversion-breakpoint junctions.
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Affiliation(s)
- Charikleia Karageorgiou
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Rosa Tarrío
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Francisco Rodríguez-Trelles
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Barcelona, Spain
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14
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Zhu B, Li C, Wang J, Li J, Li X. Elevation rather than season determines the assembly and co-occurrence patterns of soil bacterial communities in forest ecosystems of Mount Gongga. Appl Microbiol Biotechnol 2020; 104:7589-7602. [PMID: 32686007 DOI: 10.1007/s00253-020-10783-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 01/27/2023]
Abstract
Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community. KEY POINTS: • Seasonal dynamics of soil bacterial communities were studied in Mount Gongga. • The bacterial community was mainly affected by elevation rather than season. • Deterministic processes dominated bacterial community assembly. • The bacterial network was more complex but less stable at EBF than at DCF.
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Affiliation(s)
- Bingjian Zhu
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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15
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Effects of Litter Quality Diminish and Effects of Vegetation Type Develop During Litter Decomposition of Two Shrub Species in an Alpine Treeline Ecotone. Ecosystems 2020. [DOI: 10.1007/s10021-020-00512-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Els N, Greilinger M, Reisecker M, Tignat-Perrier R, Baumann-Stanzer K, Kasper-Giebl A, Sattler B, Larose C. Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria. Front Microbiol 2020; 11:980. [PMID: 32508790 PMCID: PMC7251065 DOI: 10.3389/fmicb.2020.00980] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/23/2020] [Indexed: 11/24/2022] Open
Abstract
We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphere continuously onto quartzfiber air filters using a DIGITEL high volume PM10 sampler. The bacterial and fungal communities, sequenced using Illumina MiSeq, as well as the chemical components of the atmosphere were compared to those of a late season snow profile. Results reveal strong dynamics in the composition of bacterial and fungal communities in air and snow. In fall the two compartments were similar, suggesting a strong interaction between them. The overlap diminished as the season progressed due to an evolution within the snowpack throughout winter and spring. Certain bacterial and fungal genera were only detected in air samples, which implies that a distinct air microbiome might exist. These organisms are likely not incorporated in clouds and thus not precipitated or scavenged in snow. Although snow appears to be seeded by the atmosphere, both air and snow showed differing bacterial and fungal communities and chemical composition. Season and alpha diversity were major drivers for microbial variability in snow and air, and only a few chemical markers were identified as important in explaining microbial diversity. Air microbial community variation was more related to chemical markers than snow microbial composition. For air microbial communities Cl–, TC/OC, SO42–, Mg2+, and Fe/Al, all compounds related to dust or anthropogenic activities, were identified as related to bacterial variability while dust related Ca2+ was significant in snow. The only common driver for snow and air was SO42–, a tracer for anthropogenic sources. The occurrence of chemical compounds was coupled with boundary layer injections in the free troposphere (FT). Boundary layer injections also caused the observed variations in community composition and chemistry between the two compartments. Long-term monitoring is required for a more valid insight in post-depositional selection in snow.
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Affiliation(s)
- Nora Els
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Marion Greilinger
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria.,Zentralanstalt für Meteorologie und Geodynamik (ZAMG), Vienna, Austria
| | - Michael Reisecker
- Avalanche Warning Service Tyrol, Department of Civil Protection, Federal State Government of Tyrol, Innsbruck, Austria
| | - Romie Tignat-Perrier
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, Écully, France
| | | | - Anne Kasper-Giebl
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
| | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Catherine Larose
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, Écully, France
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17
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De Gruyter J, Weedon JT, Bazot S, Dauwe S, Fernandez-Garberí PR, Geisen S, De La Motte LG, Heinesch B, Janssens IA, Leblans N, Manise T, Ogaya R, Löfvenius MO, Peñuelas J, Sigurdsson BD, Vincent G, Verbruggen E. Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities. FEMS Microbiol Ecol 2020; 96:5719567. [DOI: 10.1093/femsec/fiaa018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.
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Affiliation(s)
- Johan De Gruyter
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - James T Weedon
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
- Department of Ecological Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Stéphane Bazot
- Ecologie Systématique Evolution, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Steven Dauwe
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Pere-Roc Fernandez-Garberí
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Louis Gourlez De La Motte
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, B-5030 Gembloux, Belgium
| | - Bernard Heinesch
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, B-5030 Gembloux, Belgium
| | - Ivan A Janssens
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Niki Leblans
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Tanguy Manise
- AGROBIOCHEM Research Unit, Gembloux Agro-Bio Tech, University of Liege, B-5030 Gembloux, Belgium
| | - Romà Ogaya
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Mikaell Ottosson Löfvenius
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), SE-901 83 Umeå, Sweden
| | - Josep Peñuelas
- CREAF, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain
| | - Bjarni D Sigurdsson
- Faculty of Environmental Sciences, Agricultural University of Iceland, Hvanneyri, IS-311 Borgarnes, Iceland
| | - Gaëlle Vincent
- Ecologie Systématique Evolution, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Erik Verbruggen
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium
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18
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Baloh P, Els N, David RO, Larose C, Whitmore K, Sattler B, Grothe H. Assessment of Artificial and Natural Transport Mechanisms of Ice Nucleating Particles in an Alpine Ski Resort in Obergurgl, Austria. Front Microbiol 2019; 10:2278. [PMID: 31636618 PMCID: PMC6788259 DOI: 10.3389/fmicb.2019.02278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/18/2019] [Indexed: 01/31/2023] Open
Abstract
Artificial snow production is a crucial part of modern skiing resorts in Austria and globally, and will develop even more so with changing precipitation patterns and a warming climate trend. Producing artificial snow requires major investments in energy, water, infrastructure and manpower for skiing resorts. In addition to appropriate meteorological conditions, the efficiency of artificial snow production depends on heterogeneous ice-nucleation, which can occur at temperatures as high as -2°C when induced by specific bacterial ice nucleating particles (INPs). We aimed to investigate the presence, source and ice nucleating properties of these particles in the water cycle of an alpine ski resort in Obergurgl, Tyrol, Austria. We sampled artificial snow, river water, water pumped from a storage pond and compared it to samples collected from fresh natural snow and aged piste snow from the area. Particles from each sampled system were characterized in order to determine their transport mechanisms at a ski resort. We applied a physical droplet freezing assay [DRoplet Ice Nuclei Counter Zurich (DRINCZ)] to heated and unheated samples to characterize the biological and non-biological component of IN-activity. Bacterial abundance and community structure of the samples was obtained using quantitative PCR and Illumina Mi-Seq Amplicon Sequencing, and their chemical properties were determined by liquid ion-chromatography, energy dispersive X-ray spectroscopy (EDX) and scanning electron microscopy (SEM). The results show the flow of biological and inorganic material from the river to the slopes, an uptake of new microorganisms through the air and the piping, and possible proliferation or introduction of ice nucleation active biological particles in aged piste snow. Natural snow, as the first stage in this system, had the lowest amount of ice nucleation active particles and the least amount of biological and mineral particles in general, yet shares some microbial characteristics with fresh artificial snow.
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Affiliation(s)
- Philipp Baloh
- Institute for Materials Chemistry, TU Wien, Vienna, Austria
| | - Nora Els
- Lake and Glacier Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Robert O David
- Institute for Atmospheric and Climate Science, ETH Zürich, Zurich, Switzerland
| | - Catherine Larose
- Laboratoire Ampère, Environmental Microbial Genomics, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Karin Whitmore
- University Service Center for Transmission Electron Microscopy, TU Wien, Vienna, Austria
| | - Birgit Sattler
- Lake and Glacier Research Group, Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Hinrich Grothe
- Institute for Materials Chemistry, TU Wien, Vienna, Austria
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19
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Borg Dahl M, Brejnrod AD, Russel J, Sørensen SJ, Schnittler M. Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps. MICROBIAL ECOLOGY 2019; 78:764-780. [PMID: 30903202 DOI: 10.1007/s00248-019-01347-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
We used direct DNA amplification from soil extracts to analyze microbial communities from an elevational transect in the German Alps by parallel metabarcoding of bacteria (16S rRNA), fungi (ITS2), and myxomycetes (18S rRNA). For the three microbial groups, 5710, 6133, and 261 operational taxonomic units (OTU) were found. For the latter group, we can relate OTUs to barcodes from fruit bodies sampled over a 4-year period. The alpha diversity of myxomycetes was positively correlated with that of bacteria. Vegetation type was found to be the main explanatory parameter for the community composition of all three groups and a substantial species turnover with elevation was observed. Bacteria and fungi display similar community responses, driven by symbiont species and plant substrate quality. Myxamoebae show a more patchy distribution, though still clearly stratified between taxa, which seems to be a response to both structural properties of the habitat and interaction with specific bacterial and fungal taxa. Finally, we report a high number of myxomycete OTUs not represented in a reference database from fructifications, which might represent novel species.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany.
| | - Asker Daniel Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, 17487, Greifswald, Mecklenburg-Vorpommern, Germany
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20
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Shigyo N, Umeki K, Hirao T. Seasonal Dynamics of Soil Fungal and Bacterial Communities in Cool-Temperate Montane Forests. Front Microbiol 2019; 10:1944. [PMID: 31507559 PMCID: PMC6716449 DOI: 10.3389/fmicb.2019.01944] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/07/2019] [Indexed: 02/01/2023] Open
Abstract
Both fungal and bacterial communities in soils play key roles in driving forest ecosystem processes across multiple time scales, but how seasonal changes in environmental factors shape these microbial communities is not well understood. Here, we aimed to evaluate the importance of seasons, elevation, and soil depth in determining soil fungal and bacterial communities, given the influence of climate conditions, soil properties and plant traits. In this study, seasonal patterns of diversity and abundance did not synchronize between fungi and bacteria, where soil fertility explained the diversity and abundance of soil fungi but soil water content explained those of soil bacteria. Model-based clustering showed that seasonal changes in both abundant and rare taxonomic groups were different between soil fungi and bacteria. The cluster represented by ectomycorrhizal genus Lactarius was a dominant group across soil fungal communities and fluctuated seasonally. For soil bacteria, the clusters composed of dominant genera were seasonally stable but varied greatly depending on elevation and soil depth. Seasonally changing clusters of soil bacteria (e.g., Nitrospira and Pelosinus) were not dominant groups and were related to plant phenology. These findings suggest that the contribution of seasonal changes in climate conditions, soil fertility, and plant phenology to microbial communities might be equal to or greater than the effects of spatial heterogeneity of those factors. Our study identifies aboveground-belowground components as key factors explaining how microbial communities change during a year in forest soils at mid-to-high latitudes.
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Affiliation(s)
- Nobuhiko Shigyo
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Chichibu, Japan
| | - Kiyoshi Umeki
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Chichibu, Japan
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Praeg N, Pauli H, Illmer P. Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient. Front Microbiol 2019; 10:1429. [PMID: 31338073 PMCID: PMC6629913 DOI: 10.3389/fmicb.2019.01429] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022] Open
Abstract
Serving as “natural laboratories”, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600–3,400 m a.s.l.). The research area of this study was Mount (Mt.) “Schrankogel” in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000–3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.
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Affiliation(s)
- Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Harald Pauli
- Department of Integrative Biology and Biodiversity Research, Institute for Interdisciplinary Mountain Research and University of Natural Resources and Life Sciences Vienna, Austrian Academy of Sciences, Vienna, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
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Mania I, Gorra R, Colombo N, Freppaz M, Martin M, Anesio AM. Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. MICROBIAL ECOLOGY 2019; 78:70-84. [PMID: 30317429 DOI: 10.1007/s00248-018-1272-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4+) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.
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Affiliation(s)
- I Mania
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK.
| | - R Gorra
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - N Colombo
- Department of Earth Sciences, University of Turin, Via Valperga Caluso 35, 10125, Torino, Italy
- Department of Geography and Environmental Studies, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - M Freppaz
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - M Martin
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - A M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Department of Environmental Sciences, Aarhus University, 4000, Roskilde, Denmark
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23
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Donhauser J, Frey B. Alpine soil microbial ecology in a changing world. FEMS Microbiol Ecol 2019; 94:5017441. [PMID: 30032189 DOI: 10.1093/femsec/fiy099] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/25/2018] [Indexed: 01/22/2023] Open
Abstract
Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.
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Affiliation(s)
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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24
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Dresch P, Falbesoner J, Ennemoser C, Hittorf M, Kuhnert R, Peintner U. Emerging from the ice-fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier. Environ Microbiol 2019; 21:1864-1880. [PMID: 30888722 PMCID: PMC6849718 DOI: 10.1111/1462-2920.14598] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 11/30/2022]
Abstract
We used amplicon sequencing and isolation of fungi from in-growth mesh bags to identify active fungi in three earliest stages of soil development (SSD) at a glacier forefield (0-3, 9-14, 18-25 years after retreat of glacial ice). Soil organic matter and nutrient concentrations were extremely low, but the fungal diversity was high [220 operational taxonomic units (OTUs)/138 cultivated OTUs]. A clear successional trend was observed along SSDs, and species richness increased with time. Distinct changes in fungal community composition occurred with the advent of vascular plants. Fungal communities of recently deglaciated soil are most distinctive and rather similar to communities typical for cryoconite or ice. This indicates melting water as an important inoculum for native soil. Moreover, distinct seasonal differences were detected in fungal communities. Some fungal taxa, especially of the class Microbotryomycetes, showed a clear preference for winter and early SSD. Our results provide insight into new facets regarding the ecology of fungal taxa, for example, by showing that many fungal taxa might have an alternative, saprobial lifestyle in snow-covered, as supposed for a few biotrophic plant pathogens of class Pucciniomycetes. The isolated fungi include a high proportion of unknown species, which can be formally described and used for experimental approaches.
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Affiliation(s)
- Philipp Dresch
- Institute of MicrobiologyUniversity InnsbruckInnsbruckAustria
| | | | | | | | - Regina Kuhnert
- Institute of MicrobiologyUniversity InnsbruckInnsbruckAustria
| | - Ursula Peintner
- Institute of MicrobiologyUniversity InnsbruckInnsbruckAustria
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25
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Frindte K, Pape R, Werner K, Löffler J, Knief C. Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients. ISME JOURNAL 2019; 13:2031-2043. [PMID: 30952996 DOI: 10.1038/s41396-019-0409-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 03/01/2019] [Accepted: 03/18/2019] [Indexed: 11/09/2022]
Abstract
Microbial communities in arctic-alpine soils show biogeographic patterns related to elevation, but the effect of fine-scale heterogeneity and possibly related temperature and soil moisture regimes remains unclear. We collected soil samples from different micro-topographic positions and elevational levels in two mountain regions of the Scandes, Central Norway. Microbial community composition was characterized by 16S rRNA gene amplicon sequencing and was dependent on micro-topography and elevation. Underlying environmental drivers were identified by integration of microbial community data with a comprehensive set of site-specific long-term recorded temperature and soil moisture data. Partial least square regression analysis allowed the description of ecological response patterns and the identification of the important environmental drivers for each taxonomic group. This demonstrated for the first time that taxa responding to elevation were indeed most strongly defined by temperature, rather than by other environmental factors. Micro-topography affected taxa were primarily controlled by temperature and soil moisture. In general, 5-year datasets had higher explanatory power than 1-year datasets, indicating that the microbial community composition is dependent on long-term developments of near-ground temperature and soil moisture regimes and possesses a certain resilience, which is in agreement with an often observed delayed response in global warming studies in arctic-alpine regions.
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Affiliation(s)
- K Frindte
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, Nussallee 13, 53115, Bonn, Germany.
| | - R Pape
- Department of Geography, University of Bonn, Meckenheimer Allee 166, 53115, Bonn, Germany
| | - K Werner
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, Nussallee 13, 53115, Bonn, Germany.,Beuth Hochschule für Technik, Seestraße 64, 13347, Berlin, Germany
| | - J Löffler
- Department of Geography, University of Bonn, Meckenheimer Allee 166, 53115, Bonn, Germany
| | - C Knief
- Institute of Crop Science and Resource Conservation (INRES), Molecular Biology of the Rhizosphere, Nussallee 13, 53115, Bonn, Germany
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Young JM, Skvortsov T, Kelleher BP, Mahaney WC, Somelar P, Allen CCR. Effect of soil horizon stratigraphy on the microbial ecology of alpine paleosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:1183-1193. [PMID: 30677885 DOI: 10.1016/j.scitotenv.2018.11.442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
There is remarkable potential for research at the interface between the earth sciences and environmental microbiology that may lead to advances in our understanding of the role of bacterial communities in the surface or subsurface environment of our planet. One mainstay of sedimentary classification is the concept of differential soil and/or paleosol horizons being the result of primarily physical and chemical weathering, with relatively little understanding of how microbial communities between these stratified horizons differ, if at all. In this study we evaluate the differences in microbial community taxonomy and biogeochemical functional potential between stratified soil horizons in an alpine paleosol environment using next-generation sequencing (NGS) shotgun sequencing. Paleosols represent a unique environment to study the effect of differences soil horizon environments on the microbial community due to their relative isolation, and the fact that three distinct stratified soil horizons can be identified within the top 30 cm of the soil. This enables us to assess variation in microbial community composition that will be relatively distinct from variation due to distance alone. We test the hypothesis that variation in soil community composition is linked to variation in the physical and chemical parameters that define stratigraphy. Multivariate statistical analysis of sequencing reads from soil horizons across five sampling sites revealed that 1223 microbial genera vary significantly and consistently in abundance across stratified soil horizons at class level. Specifically Ktedonobacter, Bacilli and Betaproteobacteria responded most strongly to soil depth. Alpha diversity showed a positive correlation with soil depth. Beta diversity, however, did not differ significantly between horizons. Genes involved in carbohydrate and nitrogen metabolism were found to be more abundant in Ah horizon samples. Closer inspection of carbohydrate metabolism genes revealed that genes involved in CO2 fixation, fermentation and saccharide metabolism decreased in abundance with depth while one‑carbon metabolism increased down profile.
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27
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Chang S, Chen J, Su J, Yang Y, Sun H. Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains. PLANT DIVERSITY 2018; 40:209-216. [PMID: 30740566 PMCID: PMC6224804 DOI: 10.1016/j.pld.2018.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/08/2018] [Accepted: 09/11/2018] [Indexed: 06/09/2023]
Abstract
Positive associations between alpine cushion plants and other species have been extensively studied. However, almost all studies have focused on the associations between macrofauna. Studies that have investigated positive associations between alpine cushion plants and rhizospheric microbes have been limited to the vegetation growing season. Here, we asked whether the positive effects that alpine cushion plants confer on rhizospheric microbe communities vary with seasons. We assessed seasonal variations in the bacterial diversity and composition in rhizosphere of two alpine cushion plants and surrounding bare ground by employing a high throughput sequencing method targeting the V3 region of bacterial 16S rRNA genes. Soil properties of the rhizosphere and the bare ground were also examined. We found that cushion rhizospheres harbored significantly more C, N, S, ammonia nitrogen, and soil moisture than the bare ground. Soil properties in cushion rhizospheres were not notably different, except for soil pH. Bacterial diversities within the same microhabitats did not vary significantly with seasons. We concluded that alpine cushion plants had positive effects on the rhizospheric bacterial communities, even though the strength of the effect varied in different cushion species. Cushion species and the soil sulfur content were probably the major factors driving the spatial distribution and structure of soil bacterial communities in the alpine communities dominated by cushion plants.
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Affiliation(s)
- Shuai Chang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianguo Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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28
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Lindström S, Rowe O, Timonen S, Sundström L, Johansson H. Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques-validity and compatibility in ecological studies. PeerJ 2018; 6:e5289. [PMID: 30042898 PMCID: PMC6055595 DOI: 10.7717/peerj.5289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/01/2018] [Indexed: 11/30/2022] Open
Abstract
Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the ant Formica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.
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Affiliation(s)
- Stafva Lindström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Owen Rowe
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Sari Timonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
- Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Helena Johansson
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol 2018; 27:2461-2476. [PMID: 29675967 DOI: 10.1111/mec.14694] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 12/13/2022]
Abstract
Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function; however, our understanding of alpine soil ecology remains limited. This study aimed to (i) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to (ii) assess the impact of woody shrub expansion on these patterns. In the White Mountains of California, sagebrush (Artemisia rothrockii) shrubs have been expanding upwards into alpine areas since 1960. In this study, we combined observational field data with a manipulative shrub removal experiment along an elevation transect of alpine shrub expansion. We utilized next-generation sequencing of the ITS1 region for fungi and joint distribution modelling to tease apart effects of the environment and intracommunity interactions on soil fungi. We found that soil fungal diversity declines and community composition changes with increasing elevation. Both abiotic factors (primarily soil moisture and soil organic C) and woody sagebrush range expansion had significant effects on these patterns. However, fungal diversity and relative abundance had high spatial variation, overwhelming the predictive power of vegetation type, elevation and abiotic soil conditions at the landscape scale. Finally, we observed positive and negative associations among fungal taxa which may be important in structuring community responses to global change.
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Affiliation(s)
- Courtney G Collins
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California
| | - Sören E Weber
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California
| | - Jeffrey M Diez
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, California
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High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils. Appl Environ Microbiol 2017; 83:AEM.01139-17. [PMID: 28687652 DOI: 10.1128/aem.01139-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/30/2017] [Indexed: 11/20/2022] Open
Abstract
Glacier forefield soils can provide a substantial sink for atmospheric CH4, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH4 oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH4 flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH4 uptake rates ranging from -3.7 to -0.03 mg CH4 m-2 day-1 Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH4 emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH4 flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH4 sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH4 inventories.IMPORTANCE Oxidation of methane (CH4) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH4 oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH4 oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH4 in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH4 oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH4 inventories.
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He Z, Long X, Li L, Yu G, Chong Y, Xing W, Zhu Z. Temperature response of sulfide/ferrous oxidation and microbial community in anoxic sediments treated with calcium nitrate addition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 191:209-218. [PMID: 28104553 DOI: 10.1016/j.jenvman.2017.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 01/02/2017] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
Nitrate-driven sulfide oxidation has been proved a cost-effective way to control sediments odor which has long been a universal problem for urban rivers in south China areas. In this work, sediments treatment experiments under a dynamic variation of temperature from 5 °C to 35 °C with 3% of calcium nitrate added were conducted to reveal the influence of temperature variation on this process. The results showed that microbial community was remarkably restructured by temperature variation. Pseudomonas (15.56-29.31%), Sulfurimonas (26.81%) and Thiobacillus (37.99%) were dominant genus at temperature of ≤15 °C, 25 °C and 35 °C, respectively. It seemed that species enrichment occurring at different temperature gradient resulted in the distinct variation of microbial community structure and diversity. Moreover, nitrate-driven sulfide and ferrous oxidation were proportionally promoted only when temperature increased above 15 °C. The dominant bacteria at high temperature stage were those genus that closely related to autotrophic nitrate-driven sulfide and ferrous oxidizing bacteria (e.g.Thiobacillus, Sulfurimonas and Thermomonas), revealing that promotion of sulfide/ferrous oxidation could be attributed to the change of dominant bacteria determined by temperature variation. Thus, a higher treatment efficiency by calcium nitrate addition for odor control would be achieved in summer than any other seasons in south China areas.
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Affiliation(s)
- Zihao He
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Xinxian Long
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Luyao Li
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guangwei Yu
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China.
| | - Yunxiao Chong
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Wen Xing
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Ziao Zhu
- Department of Environmental Science and Engineering, College of Natural Resource and Environment, South China Agricultural University, Guangzhou 510642, China
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Oldham AL, Steinberg MK, Duncan KE, Makama Z, Beech I. Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes. J Ind Microbiol Biotechnol 2016; 44:167-180. [PMID: 28013395 DOI: 10.1007/s10295-016-1887-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/14/2016] [Indexed: 11/25/2022]
Abstract
Navy vessels consist of various metal alloys and biofilm accumulation at the metal surface is thought to play a role in influencing metal deterioration. To develop better strategies to monitor and control metallic biofilms, it is necessary to resolve the bacterial composition within the biofilm. This study aimed to determine if differences in electrochemical current could influence the composition of dominant bacteria in a metallic biofilm, and if so, determine the level of resolution using metagenomic amplicon sequencing. Current was generated by creating galvanic couples between cathodes made from stainless steel and anodes made from carbon steel, aluminum, or copper nickel and exposing them in the Delaware Bay. Stainless steel cathodes (SSCs) coupled to aluminum or carbon steel generated a higher mean current (0.39 mA) than that coupled to copper nickel (0.17 mA). Following 3 months of exposure, the bacterial composition of biofilms collected from the SSCs was determined and compared. Dominant bacterial taxa from the two higher current SSCs were different from that of the low-current SSC as determined by DGGE and verified by Illumina DNA-seq analysis. These results demonstrate that electrochemical current could influence the composition of dominant bacteria in metallic biofilms and that amplicon sequencing is sufficient to complement current methods used to study metallic biofilms in marine environments.
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Affiliation(s)
- Athenia L Oldham
- Department of Biology, University of Texas of the Permian Basin, 4901 E University, Odessa, TX, 79762, USA.
| | - Mia K Steinberg
- Naval Surface Warfare Center Carderock Division, 9500 Macarthur Blvd, West Bethesda, MD, 20817, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH #136, Norman, OK, 73019, USA
| | - Zakari Makama
- Department of Microbiology and Plant Biology, University of Oklahoma, 100 E Boyd, Norman, OK, 73019, USA
| | - Iwona Beech
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH #136, Norman, OK, 73019, USA
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Tang H, Shi X, Wang X, Hao H, Zhang XM, Zhang LP. Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone. Front Microbiol 2016; 7:343. [PMID: 27047461 PMCID: PMC4801888 DOI: 10.3389/fmicb.2016.00343] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/03/2016] [Indexed: 01/05/2023] Open
Abstract
The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line.
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Affiliation(s)
- Hui Tang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Xunxun Shi
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Xiaofei Wang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Huanhuan Hao
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Xiu-Min Zhang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
| | - Li-Ping Zhang
- College of Life Sciences, Hebei UniversityBaoding, China; The Key Lab of Microbial Diversity Research and Application of Hebei ProvinceBaoding, China; Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei UniversityBaoding, China
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