1
|
Wan X, Zhou R, Yuan Y, Xing W, Liu S. Microbiota associated with urban forests. PeerJ 2024; 12:e16987. [PMID: 38444615 PMCID: PMC10913776 DOI: 10.7717/peerj.16987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
Urban forests are essential for maintaining urban ecological stability. As decomposers, soil microorganisms play an indispensable role in the stability of urban forest ecosystems, promoting the material cycle of the ecosystems. This study used high-throughput sequencing technology to explore the bacteria in six forest stands, including Phyllostachys edulis (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Meanwhile, the differences in fungal communities were investigated. The results show that ZL has the highest alpha diversity of bacterial communities, while its fungal community is the lowest; Proteobacteria is the most abundant bacterial phylum in the six forest stands; ZKQ has the highest fungal diversity. In addition, soil microbial communities are affected by environmental factors. Soil pH, organic matter (SOM), and available phosphorus (AP) significantly influence the compositions of urban forest soil microbial communities. This study revealed the differences in bulk soil (BS) microbial community structures among six forest stands and the relationship between environmental factors and soil microbial communities, which has important guiding significance for creating healthy and stable urban forests with profound ecological benefits.
Collapse
Affiliation(s)
- Xin Wan
- Jiangsu Academy of Forestry, Nanjing, China
| | | | | | - Wei Xing
- Jiangsu Academy of Forestry, Nanjing, China
| | - Sian Liu
- Yangzhou University, Yangzhou, China
| |
Collapse
|
2
|
Niu B, Fu G. Response of plant diversity and soil microbial diversity to warming and increased precipitation in alpine grasslands on the Qinghai-Xizang Plateau - A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168878. [PMID: 38029973 DOI: 10.1016/j.scitotenv.2023.168878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
Plant diversity and soil microbial diversity are closely related, and they maintain the health and stability of terrestrial ecosystems. As a hotspot region of global biodiversity research, both air temperature and precipitation of the Qinghai-Xizang Plateau tend to increase in future. Based on an overview of the responses of grassland/alpine ecosystems to seasonal asymmetric warming and increased precipitation worldwide, we elaborated the advancements and uncertainties on the responses of plant diversity and soil microbial diversity to warming and increased precipitation in alpine grasslands on the Qinghai-Xizang Plateau. The future research focus of plant diversity and soil microbial diversity in the alpine grasslands of the Qinghai-Xizang Plateau under climate warming and increased precipitation was proposed. Generally, previous studies found that the responses of plant species diversity and soil microbial species diversity to warming and increased precipitation differed between alpine meadows and alpine steppes, but few studies focused on their responses to warming and increased precipitation in alpine desert steppes. Previous studies mainly focused on species diversity, although phylogenetic and functional diversities are also important aspects of biodiversity. Previous studies mainly explained responses of plant diversity and soil microbial diversity to warming and increased precipitation based on niche theory, although neutral theory is also the other important mechanism in regulating biodiversity. Moreover, previous studies almost ignored the coupling relationship between plant diversity and soil microbial diversity. Therefore, the following four aspects need to be strengthened, including the responses of plant diversity and soil microbial diversity to warming and increased precipitation in alpine desert steppes, the responses of plant and soil microbial phylogenetic diversity and functional diversity to warming and increased precipitation, combining the niche theory and neutral theory to examining the mechanism of biodiversity, and the coupling relationships between plant diversity and soil microbial diversity under warming and increased precipitation.
Collapse
Affiliation(s)
- Ben Niu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
3
|
Zhao J, Xie X, Jiang Y, Li J, Fu Q, Qiu Y, Fu X, Yao Z, Dai Z, Qiu Y, Chen H. Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168793. [PMID: 37996030 DOI: 10.1016/j.scitotenv.2023.168793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.
Collapse
Affiliation(s)
- Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xuan Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yuying Jiang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| |
Collapse
|
4
|
Bei Q, Reitz T, Schnabel B, Eisenhauer N, Schädler M, Buscot F, Heintz-Buschart A. Extreme summers impact cropland and grassland soil microbiomes. THE ISME JOURNAL 2023; 17:1589-1600. [PMID: 37419993 PMCID: PMC10504347 DOI: 10.1038/s41396-023-01470-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.
Collapse
Affiliation(s)
- Qicheng Bei
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany.
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
5
|
Sushmitha TJ, Rajeev M, Murthy PS, Rao TS, Pandian SK. Planktonic and early-stage biofilm microbiota respond contrastingly to thermal discharge-created seawater warming. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115433. [PMID: 37696079 DOI: 10.1016/j.ecoenv.2023.115433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023]
Abstract
Thermal-discharges from power plants highly disturb the biological communities of the receiving water body and understanding their influence is critical, given the relevance to global warming. We employed 16 S rRNA gene sequencing to examine the response of two dominant marine bacterial lifestyles (planktonic and biofilm) against elevated seawater temperature (+5 ℃). Obtained results demonstrated that warming prompted high heterogeneity in diversity and composition of planktonic and biofilm microbiota, albeit both communities responded contrastingly. Alpha diversity revealed that temperature exhibited positive effect on biofilm microbiota and negative effect on planktonic microbiota. The community composition of planktonic microbiota shifted significantly in warming area, with decreased abundances of Bacteroidetes, Cyanobacteria, and Actinobacteria. Contrastingly, these bacterial groups exhibited opposite trend in biofilm microbiota. Co-occurrence networks of biofilm microbiota displayed higher node diversity and co-presence in warming area. The study concludes that with increasing ocean warming, marine biofilms and biofouling management strategies will be more challenging.
Collapse
Affiliation(s)
- T J Sushmitha
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Meora Rajeev
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - P Sriyutha Murthy
- Water & Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Toleti Subba Rao
- School of Arts & Sciences, Sai University, OMR, Paiyanur, 603105 Tamil Nadu, India
| | | |
Collapse
|
6
|
Alster CJ, van de Laar A, Goodrich JP, Arcus VL, Deslippe JR, Marshall AJ, Schipper LA. Quantifying thermal adaptation of soil microbial respiration. Nat Commun 2023; 14:5459. [PMID: 37673868 PMCID: PMC10482979 DOI: 10.1038/s41467-023-41096-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
Quantifying the rate of thermal adaptation of soil microbial respiration is essential in determining potential for carbon cycle feedbacks under a warming climate. Uncertainty surrounding this topic stems in part from persistent methodological issues and difficulties isolating the interacting effects of changes in microbial community responses from changes in soil carbon availability. Here, we constructed a series of temperature response curves of microbial respiration (given unlimited substrate) using soils sampled from around New Zealand, including from a natural geothermal gradient, as a proxy for global warming. We estimated the temperature optima ([Formula: see text]) and inflection point ([Formula: see text]) of each curve and found that adaptation of microbial respiration occurred at a rate of 0.29 °C ± 0.04 1SE for [Formula: see text] and 0.27 °C ± 0.05 1SE for [Formula: see text] per degree of warming. Our results bolster previous findings indicating thermal adaptation is demonstrably offset from warming, and may help quantifying the potential for both limitation and acceleration of soil C losses depending on specific soil temperatures.
Collapse
Affiliation(s)
- Charlotte J Alster
- Te Aka Mātuatua School of Science, The University of Waikato, Hamilton, 3240, Aotearoa New Zealand.
- Department of Soil & Physical Sciences, Faculty of Agricultural & Life Sciences, Lincoln University, Lincoln, 7647, Aotearoa New Zealand.
| | - Allycia van de Laar
- Te Aka Mātuatua School of Science, The University of Waikato, Hamilton, 3240, Aotearoa New Zealand
- Manaaki Whenua-LandcareResearch, Hamilton, 3216, Aotearoa New Zealand
| | - Jordan P Goodrich
- Te Aka Mātuatua School of Science, The University of Waikato, Hamilton, 3240, Aotearoa New Zealand
- Ministry for the Environment, Wellington, 6143, Aotearoa New Zealand
| | - Vickery L Arcus
- Te Aka Mātuatua School of Science, The University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Julie R Deslippe
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6012, Aotearoa New Zealand
| | - Alexis J Marshall
- Te Aka Mātuatua School of Science, The University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Louis A Schipper
- Te Aka Mātuatua School of Science, The University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| |
Collapse
|
7
|
Lu J, Sha H, Chen J, Yi X, Xiong J. Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12572-7. [PMID: 37191684 DOI: 10.1007/s00253-023-12572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.
Collapse
Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xianghua Yi
- Lanshion Marine Science and Technology Co., Ltd, Ningbo, 315715, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
8
|
Li Z, Wang J, Wu Y, Hu J, Cong L, Yang C, Fu J, Sun J. Changes in soil properties and the phoD-harboring bacteria of the alfalfa field in response to phosphite treatment. Front Microbiol 2022; 13:1013896. [DOI: 10.3389/fmicb.2022.1013896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/02/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphite, a reduced form of orthophosphate, is characterized by high solubility, and transportation efficiency and can be used as potential phosphorus fertilizer, plant biostimulant and supplemental fertilizer in agriculture. However, the effects of phosphite fertilizer on soil properties and microorganisms are poorly understood. This study evaluated the effects of phosphate and phosphite fertilizers on the different forms of phosphorus, alkaline phosphatase (ALP) activity, and phoD-harboring bacterial community in the alfalfa (Medicago sativa) field. The study used four concentrations (30, 60, 90, and 120 mg P2O5 kg−1 soil) of phosphate (KH2PO4) and phosphite (KH2PO3) fertilizers for the alfalfa field treatment. The results showed that both phosphite and phosphate fertilizers increased the total phosphorus (TP) and available phosphorus (AP) contents in the soil. The phosphorus content of the phosphite-treated soil was lower than that of the phosphate-treated one. TP, inorganic phosphate (Pi), and AP negatively regulated ALP activity, which decreased with increasing phosphate and phosphite fertilizers concentrations. Furthermore, high-throughput sequencing analysis identified 6 phyla and 29 families, which were classified from the altered operational taxonomic units (OTUs) of the soil samples. The redundancy analysis (RDA) revealed that pH, TP, AP and Pi were significantly related to the phoD-harboring bacterial community constructure. The different fertilizer treatments altered the key families, contributing to soil ALP activities. Frankiaceae, Sphingomonadaceae, and Rhizobiaceae positively correlated with ALP activity in phosphite-treated soil. Moreover, the structural equation model (SEM) revealed that ALP activity was affected by the phoD-harboring bacterial community through altered organic phosphorus (Po), AP, total nitrogen (TN), soil organic carbon (SOC), and pH levels under phosphate fertilizer treatment. However, the effect was achieved through positive regulation of pH and AP under phosphite fertilizer. Thus, the changes in soil properties and phoD-harboring bacteria in response to phosphate and phosphite treatments differed in the alfalfa field. This study is the first to report the effects of phosphite on the soil properties of an alfalfa field and provides a strong basis for phosphite utilization in the future.Highlights– Phosphite and phosphate increase the total phosphorus and available phosphorus.– The pH was the dominant factor influencing the phoD-harboring bacterial community under phosphite fertilizer.– The response of soil properties and phoD-harboring bacterial community to phosphate and phosphite fertilizers differed in the alfalfa field.
Collapse
|
9
|
Kang P, Pan Y, Yang P, Hu J, Zhao T, Zhang Y, Ding X, Yan X. A comparison of microbial composition under three tree ecosystems using the stochastic process and network complexity approaches. Front Microbiol 2022; 13:1018077. [PMID: 36299726 PMCID: PMC9589112 DOI: 10.3389/fmicb.2022.1018077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/22/2022] [Indexed: 10/26/2023] Open
Abstract
Soil microbes act as "players" in regulating biogeochemical cycles, whereas environmental heterogeneity drives microbial community assembly patterns and is influenced by stochastic and deterministic ecological processes. Currently, the limited understanding of soil microbial community assembly patterns and interactions under temperate forest stand differences pose a challenge in studying the soil microbial involvement during the succession from coniferous to broad-leaved forests. This study investigated the changes in soil bacterial and fungal community diversity and community structure at the regional scale and identified the pathways influencing soil microbial assembly patterns and their interactions. The results showed that broad-leaved forest cover in temperate forests significantly increased soil pH, and effectively increased soil water content, total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents. Both soil bacterial and fungal alpha diversity indices were correlated with soil physicochemical properties, especially in broad-leaved forest. The bacterial and fungal community composition of coniferous forest was dominated by deterministic process (bacteria: 69.4%; fungi: 88.9%), while the bacterial community composition of broad-leaved forest was dominated by stochastic process (77.8%) and the fungal community composition was dominated by deterministic process (52.8%). Proteobacteria, Acidobacteriota, Actinobacteriota, and Verrucomicrobiota were the dominant phyla of soil bacterial communities in temperate forests. Whereas Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota were the dominant phyla of soil fungal communities in temperate forests. Most members of dominant phylum were regulated by soil physical and chemical properties. In addition, the succession from temperate coniferous forest to broad-leaved forest was conducive to maintaining the complex network of soil bacteria and fungi, and the top 20 degree of the major taxa in the network reflected the positive response of microbial interactions to the changes of soil nutrients during forest succession. This study not only shows the mechanism by which species differences in temperate forests of northern China affect soil microbial community assembly processes, but also further emphasizes the importance of the soil microbiome as a key ecosystem factor through co-occurrence network analysis.
Collapse
Affiliation(s)
- Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, Yinchuan, Ningxia, China
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan, Ningxia, China
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Pan Yang
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
| | - Jinpeng Hu
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
| | - Tongli Zhao
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
| | - Yaqi Zhang
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
| | - Xiaodong Ding
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, Yinchuan, Ningxia, China
| | - Xingfu Yan
- School of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, Yinchuan, Ningxia, China
| |
Collapse
|
10
|
Zhou J, Wang X, Xu M, Yang J, Lai XH, Jin D, Lu S, Pu J, Yang C, Zhang S, Tao Y, Zhang Z, Liu L, Xu J. Nocardioides ochotonae sp. nov., Nocardioides campestrisoli sp. nov. and Nocardioides pantholopis sp. nov., isolated from the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2022; 72. [PMID: 36208423 DOI: 10.1099/ijsem.0.005507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
Six Gram-stain-positive, aerobic and irregular-rod-shaped actinobacteria (ZJ1313T, ZJ1307, MC1495T, Y192, 603T and X2025) were isolated from the Qinghai-Tibet Plateau of China and were characterized using a polyphasic taxonomic method. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the six new strains formed three distinct clusters within the genus Nocardioides, and strains ZJ1313T and ZJ1307 were most closely related to N. solisilvae JCM 31492T (16S rRNA gene sequence similarity, 98.0 %), MC1495T and Y192 to N. houyundeii 78T (98.5 %), and 603T and X2025 to N. dokdonensis JCM 14815T (97.6 %). The digital DNA-DNA hybridization values of strains ZJ1313T, MC1495T and 603T among each other and with type strains of their closest relatives were all below the 70 % cut-off point, but values within each pair of new strains were all higher than the threshold. The major fatty acids of these strains were iso-C16 : 0, C17 : 1 ω8c or C18 : 1 ω9c. MK-8(H4) was the predominant respiratory menaquinone and ʟʟ-2,6-diaminopimelic acid was the diagnostic diamino acid. All the strains shared diphosphatidylglycerol (predominant), phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the common polar lipids, with minor difference in the types of unidentified phospholipids, glycolipids and lipids. The G+C contents based on genomic DNA of strains ZJ1313T, MC1495T and 603T were 72.5, 72.1 and 73.2 mol%, respectively. The above results suggested that strain pairs ZJ1313T/ZJ1307, MC1495T/Y192 and 603T/X2025 represent three new species of genus Nocardioides, for which the names Nocardioides ochotonae sp. nov. (ZJ1313T=GDMCC 4.177T=KCTC 49537T=JCM 34185T), Nocardioides campestrisoli sp. nov. (MC1495T=GDMCC 4.176T=KCTC 49536T=JCM 34307T) and Nocardioides pantholopis sp. nov. (603T=CGMCC 4.7510T=DSM 106494T) are proposed accordingly.
Collapse
Affiliation(s)
- Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaoxia Wang
- Central & Clinical Laboratory of Sanya People's Hospital, Sanya 572000, Hainan Province, PR China
| | - Mingchao Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu Province, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, Henan Province, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan 030001, Shanxi Province, PR China
| | - Sihui Zhang
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yuanmeihui Tao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Zehui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
- Research Institute of Public Health, Nankai University, Tianjin 300350, PR China
| |
Collapse
|
11
|
Silva I, Alves M, Malheiro C, Silva ARR, Loureiro S, Henriques I, González-Alcaraz MN. Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation. Genes (Basel) 2022; 13:genes13050850. [PMID: 35627235 PMCID: PMC9142034 DOI: 10.3390/genes13050850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 01/31/2023] Open
Abstract
We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community’s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15–25 °C or 20–30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community’s physiological profile and the bacterial community’s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20–30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome–invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.
Collapse
Affiliation(s)
- Isabel Silva
- CEF (Center for Functional Ecology), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal;
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Marta Alves
- CBQF—Center for Biotechnology and Fine Chemistry, School of Biotechnology, Portuguese Catholic University, 4169-005 Porto, Portugal;
| | - Catarina Malheiro
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Ana Rita R. Silva
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Susana Loureiro
- CESAM (Centre for Marine and Environmental Studies), Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (C.M.); (A.R.R.S.); (S.L.)
| | - Isabel Henriques
- CEF (Center for Functional Ecology), Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, 3000-456 Coimbra, Portugal;
- Correspondence: (I.H.); (M.N.G.-A.)
| | - M. Nazaret González-Alcaraz
- Department of Agricultural Engineering of the E.T.S.I.A. & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, 30203 Cartagena, Spain
- Correspondence: (I.H.); (M.N.G.-A.)
| |
Collapse
|
12
|
Muskus AM, Miltner A, Hamer U, Nowak KM. Microbial community composition and glyphosate degraders of two soils under the influence of temperature, total organic carbon and pH. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 297:118790. [PMID: 35016983 DOI: 10.1016/j.envpol.2022.118790] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/15/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Glyphosate can be degraded by soil microorganisms rapidly and is impacted by temperature and soil properties. Enhanced temperature and total organic carbon (TOC) as well as reduced pH increased the rate of 13C315N-glyphosate conversion to CO2 and biogenic non-extractable residues (bioNERs) in a Haplic Chernozem (Muskus et al., 2019) and in a Humic Cambisol (Muskus et al., 2020). To date; however, the combined effect of temperature and TOC or pH on microbial community composition and glyphosate degraders in these two soils has not been investigated. Phospholipid fatty acid [PLFA] biomarker analysis combined with 13C labeling was employed to investigate the effect of two soil properties (pH, TOC) and of three temperatures (10 °C, 20 °C, 30 °C) on soil microorganisms. Before incubation, the properties of a Haplic Chernozem and a Humic Cambisol were adjusted to obtain five treatments: (a) Control (Haplic Chernozem: 2.1% TOC and pH 6.6; Humic Cambisol: 3% TOC and pH 7.0), (b) 3% TOC (Haplic Chernozem) or 4% TOC (Humic Cambisol), (c) 4% TOC (Haplic Chernozem) or 5% TOC (Humic Cambisol), (d) pH 6.0 (Haplic Chernozem) or pH 6.5 (Humic Cambisol), and (e) pH 5.5 for both soils. All treatments were amended with 50 mg kg-1 glyphosate and incubated at 10 °C, 20 °C or 30 °C. We observed an increase in respiration, microbial biomass and glyphosate mineralization with incubation temperature. Although respiration and microbial biomass in the Humic Cambisol was higher, the microorganisms in the Haplic Chernozem were more active in glyphosate degradation. Increased TOC shifted the microbiome and the 13C-glyphosate degraders towards Gram-positive bacteria in both soils. However, the abundance of 13C-PLFAs indicative for the starvation of Gram-negative bacteria increased with increasing TOC or decreasing pH at higher temperatures. Gram-negative bacteria thus may have been involved in earlier stages of glyphosate degradation.
Collapse
Affiliation(s)
- Angelica M Muskus
- UFZ - Helmholtz-Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstr. 15, 04318, Leipzig, Germany; Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany; Pontifical Bolivarian University, Environmental Engineering Faculty, Km 7 Vía Piedecuesta, Bucaramanga, Colombia
| | - Anja Miltner
- UFZ - Helmholtz-Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstr. 15, 04318, Leipzig, Germany
| | - Ute Hamer
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Karolina M Nowak
- UFZ - Helmholtz-Centre for Environmental Research, Department of Environmental Biotechnology, Permoserstr. 15, 04318, Leipzig, Germany.
| |
Collapse
|
13
|
Wang Z, Feng K, Lu G, Yu H, Wang S, Wei Z, Dang N, Wang Y, Deng Y. Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition. Front Microbiol 2022; 13:801083. [PMID: 35283849 PMCID: PMC8908236 DOI: 10.3389/fmicb.2022.801083] [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: 10/25/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Global warming is likely to affect the underground microbial communities in various ecosystems, but the response of soil microbial communities along a vertical depth profile to global warming has been elusive. Herein, we leveraged a warming field experiment in Qinghai-Tibet Plateau grassland and investigated the community structure of prokaryotes and fungi from the upper (0-15 cm) and lower (15-30 cm) strata under ambient and elevated temperature treatments. Three-years continual warming only significantly shifted the prokaryotic community within the upper strata and there was no significant effect observed for the fungal community. Additionally, under ambient temperature, there were significant differences between the two strata in both the prokaryotic and fungal communities, but under warming, this effect was alleviated. Next, the prokaryotic and fungal community assembly processes were measured by a phylogenetic-bin-based null approach (iCAMP). Though deterministic and stochastic processes dominated the assembly of prokaryotic and fungal communities, respectively, the deterministic processes were strengthened under warming for both communities. Specifically, the increased portion of homogeneous selection, contributing to a homogenous state, led to a smaller difference between prokaryotic communities of the two soil strata under warming. The smaller difference in the stochastic process component, i.e., dispersal limitation, contributed to the similar fungal community structures between the two strata under warming. This study deepens our understanding of warming effects on grassland microbial communities and gives greater insights on the underlying mechanisms for microbial assembly between upper and lower soil strata under warming scenarios.
Collapse
Affiliation(s)
- Zhujun Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guangxin Lu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Hao Yu
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ning Dang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yingcheng Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
14
|
Wang H, Li J, Chen H, Liu H, Nie M. Enzymic moderations of bacterial and fungal communities on short- and long-term warming impacts on soil organic carbon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150197. [PMID: 34798739 DOI: 10.1016/j.scitotenv.2021.150197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities play critical roles in soil carbon-warming feedback, but our understanding of their linkages to soil carbon (C) pools in response to short- and long-term warming is deficient. Here, by conducting a meta-analysis of 150 studies, we show that short-term (<5 years) warming mainly affects soil labile carbon (LC) pools by changing bacterial community structure, while long-term (≥5 years) warming promotes the decomposition of recalcitrant C (RC) pools by increasing fungal biomass and decreasing actinobacterial biomass. Specifically, under short-term warming, significant increases in actinobacterial biomass (+15.9%) and the G+/G- ratio (+8.0%) were accompanied by an increase in carbon-degrading enzyme activities and a decrease in LC (-5.9%). Under long-term warming, the fungal biomass (+20.4%) and related POX (phenol oxidase) activity (+34.9%) increased significantly, while actinobacterial biomass (-20.1%), RC (-18.8%) and SOC (-6.7%) decreased. Meanwhile, we observed that warming impacts on soil microbial communities can be predicted by ecosystem type, the magnitude of warming, pH and elevation. Latitude and warming duration contributed the most to explaining the responses of LC and RC, respectively, across studies. Given that RC accounts for a substantial fraction of global soil C pools, the decline in RC pools greatly contributes to soil C degradation. Our findings suggest that different microbial groups may mediate the temporal dynamics of the decomposition of different soil C components and highlight that incorporating the temporal responses of soil microorganisms will improve predictions of the long-term dynamics of soil C pools in a warmer world.
Collapse
Affiliation(s)
- Hui Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Jinquan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyang Chen
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Hao Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
15
|
Dong X, Liu C, Ma D, Wu Y, Man H, Wu X, Li M, Zang S. Organic Carbon Mineralization and Bacterial Community of Active Layer Soils Response to Short-Term Warming in the Great Hing'an Mountains of Northeast China. Front Microbiol 2022; 12:802213. [PMID: 35003032 PMCID: PMC8739994 DOI: 10.3389/fmicb.2021.802213] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022] Open
Abstract
As a buffer layer for the energy and water exchange between atmosphere and permafrost, the active layer is sensitive to climate warming. Changes in the thermal state in active layer can alter soil organic carbon (SOC) dynamics. It is critical to identify the response of soil microbial communities to warming to better predict the regional carbon cycle under the background of global warming. Here, the active layer soils collected from a wetland-forest ecotone in the continuous permafrost region of Northeastern China were incubated at 5 and 15°C for 45 days. High-throughput sequencing of the 16S rRNA gene was used to examine the response of bacterial community structure to experimental warming. A total of 4148 OTUs were identified, which followed the order 15°C > 5°C > pre-incubated. Incubation temperature, soil layer and their interaction have significant effects on bacterial alpha diversity (Chao index). Bacterial communities under different temperature were clearly distinguished. Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria accounted for more than 80% of the community abundance at the phylum level. Warming decreased the relative abundance of Chloroflexi and Acidobacteria, while Actinobacteria and Proteobacteria exhibited increasing trend. At family level, the abundance of norank_o__norank_c__AD3 and Ktedonobacteraceae decreased significantly with the increase of temperature, while Micrococcaccac increased. In addition, the amount of SOC mineralization were positively correlated with the relative abundances of most bacterial phyla and SOC content. SOC content was positively correlated with the relative abundance of most bacterial phyla. Results indicate that the SOC content was the primary explanatory variable and driver of microbial regulation for SOC mineralization. Our results provide a new perspective for understanding the microbial mechanisms that accelerates SOC decomposition under warming conditions in the forest-wetland ecotone of permafrost region.
Collapse
Affiliation(s)
- Xingfeng Dong
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Chao Liu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Dalong Ma
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Yufei Wu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Haoran Man
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Xiangwen Wu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Miao Li
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| | - Shuying Zang
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, China.,Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, China
| |
Collapse
|
16
|
Yang H, Hu C. Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau. MICROBIAL ECOLOGY 2022; 83:100-113. [PMID: 33733304 DOI: 10.1007/s00248-021-01734-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl-, were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl-. Chlorophyceae and Bacillariophyceae were positively correlated with CO32-. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.
Collapse
Affiliation(s)
- Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|
17
|
Dove NC, Barnes ME, Moreland K, Graham RC, Berhe AA, Hart SC. Depth dependence of climatic controls on soil microbial community activity and composition. ISME COMMUNICATIONS 2021; 1:78. [PMID: 37938290 PMCID: PMC9723684 DOI: 10.1038/s43705-021-00081-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 05/11/2023]
Abstract
Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.
Collapse
Affiliation(s)
- Nicholas C Dove
- Environmental Systems Graduate Group, University of California, Merced, CA, 95343, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
| | - Morgan E Barnes
- Environmental Systems Graduate Group, University of California, Merced, CA, 95343, USA
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kimber Moreland
- Environmental Systems Graduate Group, University of California, Merced, CA, 95343, USA
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Robert C Graham
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Asmeret Asefaw Berhe
- Department of Life & Environmental Sciences, University of California, Merced, CA, 95343, USA
- Sierra Nevada Research Institute, Merced, CA, 95343, USA
| | - Stephen C Hart
- Department of Life & Environmental Sciences, University of California, Merced, CA, 95343, USA
- Sierra Nevada Research Institute, Merced, CA, 95343, USA
| |
Collapse
|
18
|
Zhou Y, Sun B, Xie B, Feng K, Zhang Z, Zhang Z, Li S, Du X, Zhang Q, Gu S, Song W, Wang L, Xia J, Han G, Deng Y. Warming reshaped the microbial hierarchical interactions. GLOBAL CHANGE BIOLOGY 2021; 27:6331-6347. [PMID: 34544207 DOI: 10.1111/gcb.15891] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Global warming may alter microbially mediated ecosystem functions through reshaping of microbial diversity and modified microbial interactions. Here, we examined the effects of 5-year experimental warming on different microbial hierarchical groups in a coastal nontidal soil ecosystem, including prokaryotes (i.e., bacteria and archaea), fungi, and Cercozoa, which is a widespread phylum of protists. Warming significantly altered the diversity and structure of prokaryotic and fungal communities in soil and additionally decreased the complexity of the prokaryotic network and fragmented the cercozoan network. By using the Inter-Domain Ecological Network approach, the cross-trophic interactions among prokaryotes, fungi, and Cercozoa were further investigated. Under warming, cercozoan-prokaryotic and fungal-prokaryotic bipartite networks were simplified, whereas the cercozoan-fungal network became slightly more complex. Despite simplification of the fungal-prokaryotic network, the strengthened synergistic interactions between saprotrophic fungi and certain prokaryotic groups, such as the Bacteroidetes, retained these phyla within the network under warming. In addition, the interactions within the fungal community were quite stable under warming conditions, which stabilized the interactions between fungi and prokaryotes or protists. Additionally, we found the microbial hierarchical interactions were affected by environmental stress (i.e., salinity and pH) and soil nutrients. Interestingly, the relevant microbial groups could respond to different soil properties under ambient conditions, whereas under warming these two groups tended to respond to similar soil properties, suggesting network hub species responded to certain environmental changes related to warming, and then transferred this response to their partners through trophic interactions. Finally, warming strengthened the network modules' negative association with soil organic matters through some fungal hub species, which might trigger soil carbon loss in this ecosystem. Our study provides new insights into the response and feedback of microbial hierarchical interactions under warming scenario.
Collapse
Affiliation(s)
- Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Baoyu Sun
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China
| | - Baohua Xie
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Shuzhen Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Xiongfeng Du
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Songsong Gu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jianyang Xia
- State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Guangxuan Han
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
19
|
Lu J, Zhang X, Wang C, Li M, Chen J, Xiong J. Responses of sediment resistome, virulence factors and potential pathogens to decades of antibiotics pollution in a shrimp aquafarm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148760. [PMID: 34323773 DOI: 10.1016/j.scitotenv.2021.148760] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/18/2021] [Accepted: 06/26/2021] [Indexed: 05/28/2023]
Abstract
Aquaculture ecosystem has become a hotspot of antibiotics resistance genes (ARGs) dissemination, owing to the abuse of prophylactic antibiotics. However, it is still unclear how and to what extent ARGs respond to the increasing antibiotic pollution, a trend as expected and as has occurred. Herein, a significant sediment antibiotic pollution gradient was detected along a drainage ditch after decades of shrimp aquaculture. The increasing antibiotic pollution evidently promoted the diversities and tailored the community structures of ARGs, mobile genetic elements (MGEs), virulence factors and pathogens. The profiles of ARGs and MGEs were directly altered by the concentrations of terramycin and sulphadimidine. By contrast, virulence factors were primarily affected by nutrient variables in sediment. The pathogens potentially hosted diverse virulence factors and ARGs. More than half of the detected ARGs subtypes non-linearly responded to increasing antibiotic pollution, as supported by significant tipping points. However, we screened seven antibiotic concentration discriminatory ARGs that could serve as independent variable for quantitatively diagnosing total antibiotic concentration. Co-occurrence analysis depicted that notorious aquaculture pathogens of Vibrio harveyi and V. parahaemolyticus potentially hosted ARGs that confer resistance to multiple antibiotics, while priority pathogens for humankind, e.g., Helicobacter pylori and Staphylococcus aureus, could have harbored redundant virulence factors. Collectively, the significant tipping points and antibiotic concentration-discriminatory ARGs may translate into warning index and diagnostic approach for diagnosing antibiotic pollution. Our findings provided novel insights into the interplay among ARGs, MGEs, pathogens, virulence factors and geochemical variables under the scenario of increasing antibiotic pollution.
Collapse
Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Chaohua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
20
|
Suppression of Arbuscular Mycorrhizal Fungi Aggravates the Negative Interactive Effects of Warming and Nitrogen Addition on Soil Bacterial and Fungal Diversity and Community Composition. Appl Environ Microbiol 2021; 87:e0152321. [PMID: 34469189 DOI: 10.1128/aem.01523-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the impacts of warming, nitrogen (N) addition, and suppression of arbuscular mycorrhizal fungi (AMF) on soil bacterial and fungal richness and community composition in a field experiment. AMF root colonization and the concentration of an AMF-specific phospholipid fatty acid (PLFA) were significantly reduced after the application of the fungicide benomyl as a soil drench. Warming and N addition had no independent effects but interactively decreased soil fungal richness, while warming, N addition, and AMF suppression together reduced soil bacterial richness. Soil bacterial and fungal species diversity was lower with AMF suppression, indicating that AMF suppression has a negative effect on microbial diversity. Warming and N addition decreased the net loss of plant species and the plant species richness, respectively. AMF suppression reduced plant species richness and the net gain of plant species but enhanced the net loss of plant species. Structural equation modeling (SEM) demonstrated that the soil bacterial community responded to the increased soil temperature (ST) induced by warming and the increased soil available N (AN) induced by N addition through changes in AMF colonization and plant species richness; ST directly affected the bacterial community, but AN affected both the soil bacterial and fungal communities via AMF colonization. In addition, higher mycorrhizal colonization increased the plant species richness by increasing the net gains in plant species under warming and N addition. IMPORTANCE AMF can influence the composition and diversity of plant communities. Previous studies have shown that climate warming and N deposition reduce the effectiveness of AMF. However, how AMF affect soil bacterial and fungal communities under these global change drivers is still poorly understood. A 4-year field study revealed that AMF suppression decreased bacterial and fungal diversity irrespective of warming or N addition, while AMF suppression interacted with warming or N addition to reduce bacterial and fungal richness. In addition, bacterial and fungal community compositions were determined by mycorrhizal colonization, which was regulated by soil AN and ST. These results suggest that AMF suppression can aggravate the severe losses to native soil microbial diversity and functioning caused by global changes; thus, AMF play a vital role in maintaining belowground ecosystem stability in the future.
Collapse
|
21
|
Sensitive Groups of Bacteria Dictate Microbial Functional Responses to Short-term Warming and N Input in a Semiarid Grassland. Ecosystems 2021. [DOI: 10.1007/s10021-021-00719-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
22
|
Li J, Zhu T, Singh BK, Pendall E, Li B, Fang C, Nie M. Key microorganisms mediate soil carbon-climate feedbacks in forest ecosystems. Sci Bull (Beijing) 2021; 66:2036-2044. [PMID: 36654173 DOI: 10.1016/j.scib.2021.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/05/2021] [Accepted: 03/05/2021] [Indexed: 02/03/2023]
Abstract
Soil microorganisms are known to significantly contribute to climate change through soil carbon (C) cycle feedbacks. However, it is challenging to incorporate these feedbacks into predictions of future patterns of terrestrial C cycling, largely because of the vast diversity of soil microorganisms and their responses to environmental conditions. Here, we show that the composition of the bacterial community can provide information about the microbial community-level thermal response (MCTR), which drives ecosystem-scale soil C-climate feedbacks. The dominant taxa from 169 sites representing a gradient from tropical to boreal forest mainly belonged to the phyla Actinobacteria and Acidobacteria. Moreover, we show that the MCTR in warm biomes and acidic soils was linked primarily to bacteria, whereas the MCTR in cold biomes and alkaline soils was primarily associated with fungi. Our results provide strong empirical evidence of linkages between microbial composition and the MCTR across a wide range of forests, and suggest the importance of specific microorganisms in regulating soil C-climate feedbacks.
Collapse
Affiliation(s)
- Jinquan Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Zhu
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia; Global Centre for Land-Based Innovation, Western Sydney University, Penrith NSW 2751, Australia
| | - Elise Pendall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW 2751, Australia
| | - Bo Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Changming Fang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ming Nie
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuarine, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
23
|
Mu Z, Dong S, Li Y, Li S, Shen H, Zhang J, Han Y, Xu Y, Zhao Z. Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.709518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.
Collapse
|
24
|
Wang R, Wang M, Wang J, Lin Y. Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau. Microorganisms 2021; 9:microorganisms9081595. [PMID: 34442674 PMCID: PMC8400953 DOI: 10.3390/microorganisms9081595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.
Collapse
Affiliation(s)
- Rui Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Miao Wang
- Party School of the Chengdu Committee of the Chinese Communist Party, Chengdu 610110, China;
| | - Jing Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Yinghua Lin
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
- Correspondence: ; Tel.: +86-13671160455
| |
Collapse
|
25
|
Zhou J, Xu M, Guo W, Yang J, Pu J, Lai XH, Jin D, Lu S, Zhang S, Huang Y, Zhu W, Huang Y, Zheng H, Xu J. Corynebacterium lizhenjunii sp. nov., isolated from the respiratory tract of Marmota himalayana, and Corynebacterium qintianiae sp. nov., isolated from the lung tissue of Pseudois nayaur. Int J Syst Evol Microbiol 2021; 71. [PMID: 33974533 DOI: 10.1099/ijsem.0.004803] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-stain-positive, non-motile and asporous bacilli (strains ZJ-599T, ZJ-621, MC1420T and MC1482), isolated from animal tissue and environmental samples collected on the Qinghai-Tibet Plateau, PR China, were taxonomically characterized. Based on the results of 16S rRNA gene sequence analyses, the closest relatives of strains ZJ-599T and ZJ-621 were Corynebacterium endometrii LMM-1653T (97.5 %), Corynebacterium phocae M408/89/1T (96.5 %) and Corynebacterium flavescens OJ8T (96.3 %), whereas strains MC1420T and MC1482 were closest to Corynebacterium sanguinis CCUG 58655T (98.9 %), Corynebacterium mycetoides DSM 20632T (98.4 %) and Corynebacterium lipophiloflavum DSM 44291T (97.9 %). The results of rpoB gene sequence similarity analysis indicated that C. phocae M408/89/1T and C. sanguinis CCUG 58655T were closest to strains ZJ-599T/ZJ-621 (83.5 %) and MC1420T/MC1482 (91.8 %), respectively. The two novel type strains shared a similarity of 95.2 % in 16S rRNA and 81.3 % in rpoB gene sequences. The TAP-PCR DNA fingerprint and MALDI-TOF MS spectrum patterns clearly differentiated the novel isolates within and between each pair of strains. Strain ZJ-599T had 21.9-22.4 % digital DNA-DNA hybridization (dDDH) scores with C. endometrii LMM-1653T, C. phocae M408/89/1T and C. flavescens OJ8T, and 72.3-72.9 % of average nucleotide identity (ANI) with them. Similarly, strain MC1420T had 22.9-23.7 % dDDH values with C. sanguinis CCUG 58655T, C. mycetoides DSM 20632T and C. lipophiloflavum DSM 44291T, and 80.4-81.3 % ANI scores with them. Strain ZJ-599T had a 23.1 % dDDH value and 70.5 % ANI score with strain MC1420T, both below the corresponding thresholds for species delineation. Strains ZJ-599T and MC1420T both contain mycolic acids and have MK-8(H2) and MK-9(H2) as the predominant respiratory quinones, meso-diaminopimelic acid as the diagnostic diamino acid, and C18 : 1 ω9c as the main fatty acid. C17 : 1 ω8c and C15 : 1 ω8c were predominant in strain ZJ-599T in contrast to C17 : 1 ω7c being predominant in strain MC1420T. The main polar lipids in strain ZJ-599T were diphosphatidylglycerol, phosphatidylinositol and one unidentified glycolipid, while strain MC1420T had diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid as the major components. Since the two pairs of novel strains (ZJ-599T/ZJ-621, MC1420T/MC1482) distinctly differ from each other and from their nearest relatives, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium lizhenjunii (type strain ZJ-599T=GDMCC 1.1779T=JCM 34341T) and Corynebacterium qintianiae (type strain MC1420T=GDMCC 1.1783T=JCM 34340T), respectively.
Collapse
Affiliation(s)
- Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Mingchao Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu Province, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wentao Guo
- Qinghai Province Institute for Endemic Diseases Prevention and Control, Xining 811602, Qinghai Province, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, Henan Province, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| |
Collapse
|
26
|
Miao S, Qiao Y, Jin J, Wang Y, Tang C. Greater variation of bacterial community structure in soybean- than maize-grown Mollisol soils in responses to seven-year elevated CO 2 and temperature. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142836. [PMID: 33160664 DOI: 10.1016/j.scitotenv.2020.142836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/12/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Changes in rhizodeposits of crops under elevated CO2 (eCO2) and elevated temperature (eT) may substantially impact on soil microbial community, which in turn affects soil carbon and nutrient cycling. However, the responses of soil bacterial community to long-term eCO2 and eT are not fully understood. A seven-year field experiment using open-top chambers was carried out with soybean (Glycine max L. Merr.) and maize (Zea mays L.) grown in a Mollisol soil under ambient CO2 (380 ppm), eT (2.1 °C increase in air temperature) and eTeCO2 (elevated temperature plus elevated CO2, 2.1 °C increase in air temperature and 700 ppm CO2). Soil DNA was extracted for Illumina MiSeq sequencing. The principal coordinate analysis showed that changes of bacterial community structure due to eT and eTeCO2 were greater in soybean- than maize-grown soils. The eT increased the relative abundances of Gaiella and Bacillus in Actinobacteria and Firmicutes, but decreased those of Nocardioides and H16 in Actinobacteria and Proteobacteria, respectively. The magnitudes of responses of seven genera sensitive to eT varied between soybean- and maize-grown soils. The eTeCO2 decreased the relative abundance of Bacillus and increased those of Gaiella, Streptomyces and Mizugakiibacter. The abundances of Gaiella, Gemmatimonas, and Mizugakiibacter under eTeCO2 were higher in soybean- than maize-grown soils. The redundancy analysis showed that soil organic C, moisture, nitrate, microbial biomass N and Olsen-P significantly affected soil bacterial community composition. All these results indicate that long-term eT increased the abundance of bacterial community and shifted their composition compared to the ambient control. In addition, the bacterial community composition under eTeCO2 was more stable in maize- than soybean-grown soils. The study suggests that warming and crop species may interactively affect the stability of bacterial community linking to the sustainability of soil eco-function in future cropping systems.
Collapse
Affiliation(s)
- Shujie Miao
- School of Applied Meteorology, Nanjing University of Information Science & Technology, No. 219 Ningliu Road, Nanjing 210044, China
| | - Yunfa Qiao
- School of Applied Meteorology, Nanjing University of Information Science & Technology, No. 219 Ningliu Road, Nanjing 210044, China
| | - Jian Jin
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; Department of Animal, Plant & Soil Sciences, Centre for AgriBioscience, La Trobe University (Melbourne Campus), Bundoora, Vic 3086, Australia.
| | - Yanhong Wang
- Experimental Center, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Caixian Tang
- Department of Animal, Plant & Soil Sciences, Centre for AgriBioscience, La Trobe University (Melbourne Campus), Bundoora, Vic 3086, Australia
| |
Collapse
|
27
|
Buckley HL, Day NJ, Case BS, Lear G. Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size. PeerJ 2021; 9:e11096. [PMID: 33889442 PMCID: PMC8038644 DOI: 10.7717/peerj.11096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/22/2021] [Indexed: 12/03/2022] Open
Abstract
Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.
Collapse
Affiliation(s)
- Hannah L. Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Nicola J. Day
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Bradley S. Case
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| |
Collapse
|
28
|
Response of Soil Microbial Communities to Warming and Clipping in Alpine Meadows in Northern Tibet. SUSTAINABILITY 2020. [DOI: 10.3390/su12145617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In order to explore responses of soil microbial communities among different alpine meadows under warming and clipping, soil microorganisms of three alpine meadow sites (low altitude: 4313 m, alpine steppe meadow, 30°30′ N, 91°04′ E; mid-altitude: 4513 m, alpine steppe meadow, 30°31′ N, 91°04′ E; and high altitude: 4693, alpine Kobresia meadow, 30°32′ N, 91°03′ E) were measured using the phospholipid fatty acid (PLFA) method. Both warming and clipping significantly reduced PLFA content and changed the community composition of soil microbial taxa, which belong to bacterial and fungal communities in the alpine Kobresia meadow. Warming significantly reduced the soil total PLFA content by 36.1% and the content of soil fungi by 37.0%; the clipping significantly reduced the soil total PLFA content by 57.4%, the content of soil fungi by 49.9%, and the content of soil bacteria by 60.5% in the alpine Kobresia meadow. Only clipping changed the total fungal community composition at a low altitude. Neither clipping nor warming changed the microbial community composition at a moderate altitude. Soil temperature, soil moisture, and pH were the main factors affecting soil microbial communities. Therefore, the effects of warming and clipping on soil microbial communities in alpine meadows were related to grassland types and soil environmental conditions.
Collapse
|
29
|
Chen Q, Niu B, Hu Y, Luo T, Zhang G. Warming and increased precipitation indirectly affect the composition and turnover of labile-fraction soil organic matter by directly affecting vegetation and microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136787. [PMID: 31982765 DOI: 10.1016/j.scitotenv.2020.136787] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Global warming accompanied by precipitation changes impacts soil carbon sequestration. A three-year field manipulation experiment with warming (+2 °C above ambient temperature) and increased precipitation (+15% and +30% above ambient precipitation) was conducted in an alpine grassland to investigate the response of soil organic matter (SOM) to future climate change on the Qinghai-Tibet Plateau (QTP). Labile-fraction SOM (LF-SOM) fingerprints were characterized by pyrolysis-gas chromatography/tandem-mass spectrometry (Py-GC-MS/MS), and organic compounds in LF-SOM were used as indicators to quantify the contributions of vegetation input and microbial degradation to LF-SOM transformation. Increased precipitation promoted LF-SOM accumulation, which were mainly due to the positive effect of increased precipitation on vegetation productivity. Plant-derived compounds in LF-SOM (including lignin, long-chain alkyl compounds, polysaccharides and phenols) were more sensitive to increasing soil moisture than microbial-derived (including short-chain alkyl compounds, N compounds and chitin) and aromatic-derived compounds (including aromatics and polyaromatics). In contrast, warming alone intensified the effect of drought on the alpine grassland, which had negative effects on both vegetation and microorganisms and reduced LF-SOM. Warming plus increased precipitation not only alleviated the water loss caused by warming but also increased soil temperature, which was more favorable for the growth of microorganisms. This was reflected in the increase in microbial-derived compounds in LF-SOM with increasing soil temperature, which contributed to LF-SOM degradation. Aromatic-derived compounds, as refractory compounds in soil, showed no significant response to either warming or increased precipitation treatments. Acidobacteria (approximately 25%) and Actinobacteria (approximately 20%), as the dominant soil bacterial communities in the alpine grassland, were significantly correlated with plant-derived compounds. At the same time, there were significant correlations between Proteobacteria and microbial-derived compounds, as well as between Firmicutes and aromatic-derived compounds (relative abundance). Under future climate change, microbial activity will increase as temperature increases, which will promote LF-SOM degradation only if precipitation also increases.
Collapse
Affiliation(s)
- Qiuyu Chen
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing 100101, China; Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Bin Niu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yilun Hu
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 10049, China
| | - Tianxiang Luo
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing 100101, China
| | - Gengxin Zhang
- Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, China Academy of Sciences, Beijing 100101, China; Key Laboratory of Alpine Ecology (LAE), CAS Center for Excellence in Tibetan Plateau Earth Sciences and Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
30
|
Wu R, Chai B, Cole JR, Gunturu SK, Guo X, Tian R, Gu JD, Zhou J, Tiedje JM. Targeted assemblies of cas1 suggest CRISPR-Cas's response to soil warming. ISME JOURNAL 2020; 14:1651-1662. [PMID: 32221408 PMCID: PMC7305122 DOI: 10.1038/s41396-020-0635-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023]
Abstract
There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.
Collapse
Affiliation(s)
- Ruonan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China.,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Santosh K Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Xue Guo
- Department of Microbiology & Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Renmao Tian
- Department of Microbiology & Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, USA
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SAR, China
| | - Jizhong Zhou
- Department of Microbiology & Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. .,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
31
|
Li W, Chen H, Yan Z, Yang G, Rui J, Wu N, He Y. Variation in the Soil Prokaryotic Community Under Simulated Warming and Rainfall Reduction in Different Water Table Peatlands of the Zoige Plateau. Front Microbiol 2020; 11:343. [PMID: 32256463 PMCID: PMC7093333 DOI: 10.3389/fmicb.2020.00343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Climate change and water table drawdown impact the community structure and diversity of peatland soil prokaryotes. Nonetheless, how soil prokaryotes of different water tables respond to climate change remains largely unknown. This study used 16S rRNA gene sequencing to evaluate the variation in soil prokaryotes under scenarios of warming, rainfall reduction, and their combination in different water table peatlands on the Zoige Plateau in China. Stimulated climate change affected some of the diversity indexes and relative abundances of soil prokaryotes in three water table peatlands. Additionally, those from the dry-rewetting event peatland had the most dominant phyla (genera) that showed significant changes in a relative abundance due to the simulated climate change treatments. Regarding functional microbial groups of carbon and nitrogen cycling, simulated climate change did not affect the abundances of the Euryarchaeota, Proteobacteria, Verrucomicrobia, and Methanobacterium in three water table peatlands, except NC10 and Nitrospirae. Redundancy analysis showed that the prokaryotic community variation was primary impacted by site properties of the different water table peatlands rather than the simulated climate change treatments. Moreover, the water table, total carbon, total nitrogen, and soil pH were the primary factors for the overall variation in the soil prokaryotic structure. This study provides a theoretical guidance for management strategies in the Zoige peatland, under climate change scenarios. More attention should be given to the interactive effects of peatland water table drawdown and simulated climate changes for better restorative efforts in water table drawdown, rather than simply adapting to climate change.
Collapse
Affiliation(s)
- Wei Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
- School of Ecology and Environmental Sciences and Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
- Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhiying Yan
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Gang Yang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Junpeng Rui
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ning Wu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
| | - Yixin He
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, China
| |
Collapse
|
32
|
Xuan L, Sheng Z, Lu J, Qiu Q, Chen J, Xiong J. Bacterioplankton community responses and the potential ecological thresholds along disturbance gradients. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 696:134015. [PMID: 31470324 DOI: 10.1016/j.scitotenv.2019.134015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/24/2019] [Accepted: 08/19/2019] [Indexed: 05/28/2023]
Abstract
Increasing intensity and frequency of coastal pollutions are the trajectory to be expected due to anthropogenic pressures. However, it is still unclear how and to what extent bacterioplankton communities respond to the two factors, despite the functional importance of bacterioplankton in biogeochemical cycles. In this study, significant organic pollution index (OPI) and offshore distance gradients, as respective proxies of disturbance intensity and disturbance frequency, were detected in a regional scale across the East China Sea. A multiple regression on matrices (MRM) revealed that the biogeography of bacterioplankton community depended on spatial scale, which was governed by local characters. Bacterioplankton community compositions (BCCs) were primarily governed by the conjointly direct (-0.28) and indirect (-0.48) effects of OPI, while offshore distance contributed a large indirectly effect (0.52). A SEGMENTED analysis depicted non-linear responses of BCCs to increasing disturbance intensity and disturbance frequency, as evidenced by significant tipping points. This was also true for the dominant bacterial phyla. Notably, we screened 30 OPI-discriminatory taxa that could quantitatively diagnose coastal OPI levels, with an overall 79.3% accuracy. Collectively, the buffer capacity of bacterioplankton communities to increasing disturbance intensity and disturbance frequency is limited, of which the significant tipping points afford a warning line for coastal management. In addition, coastal pollution level can be accurately diagnosed by a few OPI-discriminatory taxa.
Collapse
Affiliation(s)
- Lixia Xuan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Zheliang Sheng
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| |
Collapse
|
34
|
Zhao P, Bao J, Wang X, Liu Y, Li C, Chai B. Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau. PeerJ 2019; 7:e6746. [PMID: 31119067 PMCID: PMC6510221 DOI: 10.7717/peerj.6746] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/08/2019] [Indexed: 01/08/2023] Open
Abstract
Microbial community assembly is influenced by a continuum (actually the trade-off) between deterministic and stochastic processes. An understanding of this ecological continuum is of great significance for drawing inferences about the effects of community assembly processes on microbial community structure and function. Here, we investigated the driving forces of soil microbial community assembly in three different environmental contexts located on subalpine coniferous forests of the Loess Plateau in Shanxi, China. The variation in null deviations and phylogenetic analysis showed that a continuum existed between deterministic and stochastic processes in shaping the microbial community structure, but deterministic processes prevailed. By integrating the results of redundancy analysis (RDA), multiple regression tree (MRT) analysis and correlation analysis, we found that soil organic carbon (SOC) was the main driver of the community structure and diversity patterns. In addition, we also found that SOC had a great influence on the community assembly processes. In conclusion, our results show that deterministic processes always dominated assembly processes in shaping bacterial community structure along the three habitat contexts.
Collapse
Affiliation(s)
- Pengyu Zhao
- Institute of Loess Plateau, Shanxi University; Shanxi Key laboratory of Ecological Restoration of Loess Plateau, Taiyuan, China
| | - Jiabing Bao
- Institute of Loess Plateau, Shanxi University; Shanxi Key laboratory of Ecological Restoration of Loess Plateau, Taiyuan, China
| | - Xue Wang
- Institute of Loess Plateau, Shanxi University; Shanxi Key laboratory of Ecological Restoration of Loess Plateau, Taiyuan, China
| | - Yi Liu
- College of Resources and Environment, Shanxi University of Finance and Economics, Taiyuan, China
| | - Cui Li
- College of Resources and Environment, Shanxi University of Finance and Economics, Taiyuan, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University; Shanxi Key laboratory of Ecological Restoration of Loess Plateau, Taiyuan, China
| |
Collapse
|
35
|
Luláková P, Perez-Mon C, Šantrůčková H, Ruethi J, Frey B. High-Alpine Permafrost and Active-Layer Soil Microbiomes Differ in Their Response to Elevated Temperatures. Front Microbiol 2019; 10:668. [PMID: 31001236 PMCID: PMC6456652 DOI: 10.3389/fmicb.2019.00668] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 03/18/2019] [Indexed: 02/01/2023] Open
Abstract
The response of microbial communities to the predicted rising temperatures in alpine regions might be an important part of the ability of these ecosystems to deal with climate change. Soil microbial communities might be significantly affected by elevated temperatures, which influence the functioning of soils within high-alpine ecosystems. To evaluate the potential of the permafrost microbiome to adapt to short-term moderate and extreme warming, we set up an incubation experiment with permafrost and active soil layers from northern and southern slopes of a high-alpine mountain ridge on Muot da Barba Peider in the Swiss Alps. Soils were acclimated to increasing temperatures (4–40°C) for 26 days before being exposed to a heat shock treatment of 40°C for 4 days. Alpha-diversity in all soils increased slightly under gradual warming, from 4 to 25°C, but then dropped considerably at 40°C. Similarly, heat shock induced strong changes in microbial community structures and functioning in the active layer of soils from both northern and southern slope aspects. In contrast, permafrost soils showed only minor changes in their microbial community structures and no changes in their functioning, except regarding specific respiration activity. Shifts in microbial community structures with increasing temperature were significantly more pronounced for bacteria than for fungi, regardless of the soil origin, suggesting higher resistance of high-alpine fungi to short-term warming. Firmicutes, mainly represented by Tumebacillus and Alicyclobacillaceae OTUs, increased strongly at 40°C in active layer soils, reaching almost 50% of the total abundance. In contrast, Saccharibacteria decreased significantly with increasing temperature across all soil samples. Overall, our study highlights the divergent responses of fungal and bacterial communities to increased temperature. Fungi were highly resistant to increased temperatures compared to bacteria, and permafrost communities showed surprisingly low response to rising temperature. The unique responses were related to both site aspect and soil origin indicating that distinct differences within high-alpine soils may be driven by substrate limitation and legacy effects of soil temperatures at the field site.
Collapse
Affiliation(s)
- Petra Luláková
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.,Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Hana Šantrůčková
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Joel Ruethi
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| |
Collapse
|
36
|
Yu C, Han F, Fu G. Effects of 7 years experimental warming on soil bacterial and fungal community structure in the Northern Tibet alpine meadow at three elevations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:814-822. [PMID: 30481708 DOI: 10.1016/j.scitotenv.2018.11.309] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 05/15/2023]
Abstract
A warming experiment was established along an altitudinal gradient (low elevation: 4313 m, mid-elevation: 4513 m and high elevation: 4693 m) in alpine meadows of the Northern Tibet to investigate the effects of warming on soil bacterial and fungal community structure. Elevation had significant effects on vegetation community coverage (CC), soil temperature (Ts) and pH, but not soil fungal diversity. Soil bacterial diversity at the high elevation was significantly lower than that at the low and mid-elevations, whereas there was no significant difference of soil bacterial diversity between the low and mid-elevations. After seven years of warming, soil fungal diversity was significantly increased at the mid-elevation but not the low and high elevations, and soil bacterial diversity was not significantly altered at the low, mid- and high elevations. Soil bacterial community structure was significantly altered at the low and mid-elevations but not the high elevation. Soil fungal community structure was significantly altered at all the three elevations. CC, Ts and pH significantly explained 20.55%, 5.30% and 12.61% of the variation of bacterial community structure, respectively. CC and Ts significantly explained 17.40% and 5.86% of the variation of fungal community structure, respectively. Therefore, responses of soil microbial community structure to warming may vary with elevation, which was mainly attributed to different vegetation coverage, soil temperature and/or pH conditions among the three elevations in this study alpine meadows.
Collapse
Affiliation(s)
- Chengqun Yu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Fusong Han
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
37
|
Effect of Freeze-Thaw on a Midtemperate Soil Bacterial Community and the Correlation Network of Its Members. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8412429. [PMID: 30050943 PMCID: PMC6040300 DOI: 10.1155/2018/8412429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/17/2018] [Indexed: 11/17/2022]
Abstract
Freeze-thaw (FT) events can influence soil functions. However, the overall impact of FTs on soil bacterial communities, especially in temperate regions, remains unclear. In this study, soil samples were collected from a midtemperate region in the northeast of China, and three incubation tests were then designed with varied FT amplitudes (i.e., at a freezing temperature of −15, −9, and −3°C, respectively), frequencies of FT cycles (i.e., under one, six, and 15 FT cycles, respectively) and soil water content (SWC) values (i.e., at 10 and 30% SWC, respectively). High-throughput sequencing of 16S rRNA gene amplicons was performed and the functional profile was further predicted based on these data, in addition to examinations of bulk microbial properties. Data analyses suggested that, first of all, the FT amplitude significantly influenced the bulk microbial properties and bacterial community (composition and function); certain taxa showed a nonlinear response to the three amplitudes. Next, compared to a single FTC, multiple FT cycles had only minor effects on the bacterial functional capabilities, although the bulk microbial properties changed significantly after multiple FT cycles. In addition, the bacterial response to FTs was influenced by the SWC, characterized by the significantly different bacterial community structures (composition and function) and the opposite trends of enzyme activities. Finally, RDA plots and a correlation network assembled data from all soil samples across the three tests and suggested that bacterial response trajectories changed because some species were influenced mainly by other species (i.e., biotic environment) during FT processes.
Collapse
|
38
|
Ma Z, Zhao W, Zhao C, Wang D, Liu M, Li D, Liu Q. Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem. PLoS One 2018; 13:e0195079. [PMID: 29668711 PMCID: PMC5905891 DOI: 10.1371/journal.pone.0195079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 03/16/2018] [Indexed: 11/18/2022] Open
Abstract
Information on how soil microbial communities respond to warming is still scarce for alpine scrub ecosystems. We conducted a field experiment with two plant treatments (plant removal or undisturbed) subjected to warmed or unwarmed conditions to examine the effects of warming and plant removal on soil microbial community structures during the growing season in a Sibiraea angustata scrubland of the eastern Qinghai–Tibetan Plateau. The results indicate that experimental warming significantly influenced soil microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), but the warming effects were dependent on the plant treatments and sampling seasons. In the plant-removal plots, warming did not affect most of the microbial variables, while in the undisturbed plots, warming significantly increased the abundances of actinomycete and Gram-positive bacterial groups during the mid-growing season (July), but it did not affect the fungi groups. Plant removal significantly reduced fungal abundance throughout the growing season and significantly altered the soil microbial community structure in July. The interaction between warming and plant removal significantly influenced the soil MBC and MBN and the abundances of total microbes, bacteria and actinomycete throughout the growing season. Experimental warming significantly reduced the abundance of rare taxa, while the interaction between warming and plant removal tended to have strong effects on the abundant taxa. These findings suggest that the responses of soil microbial communities to warming are regulated by plant communities. These results provide new insights into how soil microbial community structure responds to climatic warming in alpine scrub ecosystems.
Collapse
Affiliation(s)
- Zhiliang Ma
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Zhao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Chunzhang Zhao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Dong Wang
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Mei Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Dandan Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Qing Liu
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
- * E-mail:
| |
Collapse
|
39
|
Radujkovic D, Verbruggen E, Sigurdsson BD, Leblans NIW, Janssens IA, Vicca S, Weedon JT. Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients. FEMS Microbiol Ecol 2018; 94:4712010. [PMID: 29228354 DOI: 10.1101/102459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 05/26/2023] Open
Abstract
Global change is expected to affect soil microbial communities through their responsiveness to temperature. It has been proposed that prolonged exposure to elevated temperatures may lead to progressively larger effects on soil microbial community composition. However, due to the relatively short-term nature of most warming experiments, this idea has been challenging to evaluate. The present study took the advantage of natural geothermal gradients (from +1°C to +19°C above ambient) in two subarctic grasslands to test the hypothesis that long-term exposure (>50 years) intensifies the effect of warming on microbial community composition compared to short-term exposure (5-7 years). Community profiles from amplicon sequencing of bacterial and fungal rRNA genes did not support this hypothesis: significant changes relative to ambient were observed only starting from the warming intensity of +9°C in the long term and +7°C/+3°C in the short term, for bacteria and fungi, respectively. Our results suggest that microbial communities in high-latitude grasslands will not undergo lasting shifts in community composition under the warming predicted for the coming 100 years (+2.2°C to +8.3°C).
Collapse
Affiliation(s)
- Dajana Radujkovic
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - Erik Verbruggen
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - Bjarni D Sigurdsson
- Faculty of Environmental Sciences, Agricultural University of Iceland, Hvanneyr IS - 311 Borgarnes, Iceland
| | - Niki I W Leblans
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
- Faculty of Environmental Sciences, Agricultural University of Iceland, Hvanneyr IS - 311 Borgarnes, Iceland
| | - Ivan A Janssens
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - Sara Vicca
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
| | - James T Weedon
- Plants and Ecosystems, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk 2610, Belgium
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
40
|
Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients. FEMS Microbiol Ecol 2017; 94:4712010. [DOI: 10.1093/femsec/fix174] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/01/2017] [Indexed: 01/03/2023] Open
|
41
|
Bai Z, Xie H, Kao-Kniffin J, Chen B, Shao P, Liang C. Shifts in microbial trophic strategy explain different temperature sensitivity of CO2 flux under constant and diurnally varying temperature regimes. FEMS Microbiol Ecol 2017; 93:3814241. [PMID: 28499007 DOI: 10.1093/femsec/fix063] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/09/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding soil CO2 flux temperature sensitivity (Q10) is critical for predicting ecosystem-level responses to climate change. Yet, the effects of warming on microbial CO2 respiration still remain poorly understood under current Earth system models, partly as a result of thermal acclimation of organic matter decomposition. We conducted a 117-day incubation experiment under constant and diurnally varying temperature treatments based on four forest soils varying in vegetation stand and soil horizon. Our results showed that Q10 was greater under varying than constant temperature regimes. This distinction was most likely attributed to differences in the depletion of available carbon between constant high and varying high-temperature treatments, resulting in significantly higher rates of heterotrophic respiration in the varying high-temperature regime. Based on 16S rRNA gene sequencing data using Illumina, the varying high-temperature regime harbored higher prokaryotic alpha-diversity, was more dominated by the copiotrophic strategists and sustained a distinct community composition, in comparison to the constant-high treatment. We found a tightly coupled relationship between Q10 and microbial trophic guilds: the copiotrophic prokaryotes responded positively with high Q10 values, while the oligotrophs showed a negative response. Effects of vegetation stand and soil horizon consistently supported that the copiotrophic vs oligotrophic strategists determine the thermal sensitivity of CO2 flux. Our observations suggest that incorporating prokaryotic functional traits, such as shifts between copiotrophy and oligotrophy, is fundamental to our understanding of thermal acclimation of microbially mediated soil organic carbon cycling. Inclusion of microbial functional shifts may provide the potential to improve our projections of responses in microbial community and CO2 efflux to a changing environment in forest ecosystems.
Collapse
Affiliation(s)
- Zhen Bai
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongtu Xie
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengshuai Shao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| |
Collapse
|
42
|
Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest. Ecosphere 2017. [DOI: 10.1002/ecs2.1879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
|
43
|
McGee CF, Storey S, Clipson N, Doyle E. Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:449-458. [PMID: 28197855 DOI: 10.1007/s10646-017-1776-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/04/2017] [Indexed: 05/14/2023]
Abstract
Soil microorganisms are key contributors to nutrient cycling and are essential for the maintenance of healthy soils and sustainable agriculture. Although the antimicrobial effects of a broad range of nanoparticulate substances have been characterised in vitro, little is known about the impact of these compounds on microbial communities in environments such as soil. In this study, the effect of three widely used nanoparticulates (silver, silicon dioxide and aluminium oxide) on bacterial and fungal communities in an agricultural pastureland soil was examined in a microcosm-based experiment using a combination of enzyme analysis, molecular fingerprinting and amplicon sequencing. A relatively low concentration of silver nanoparticles (AgNPs) significantly reduced total soil dehydrogenase and urease activity, while Al2O3 and SiO2 nanoparticles had no effect. Amplicon sequencing revealed substantial shifts in bacterial community composition in soils amended with AgNPs, with significant decreases in the relative abundance of Acidobacteria and Verrucomicrobia and an increase in Proteobacteria. In particular, the relative abundance of the Proteobacterial genus Dyella significantly increased in AgNP amended soil. The effects of Al2O3 and SiO2 NPs on bacterial community composition were less pronounced. AgNPs significantly reduced bacterial and archaeal amoA gene abundance in soil, with the archaea more susceptible than bacteria. AgNPs also significantly impacted soil fungal community structure, while Al2O3 and SiO2 NPs had no effect. Several fungal ribotypes increased in soil amended with AgNPs, compared to control soil. This study highlights the need to consider the effects of individual nanoparticles on soil microbial communities when assessing their environmental impact.
Collapse
Affiliation(s)
- C F McGee
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Storey
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - N Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - E Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| |
Collapse
|
44
|
Weedon JT, Kowalchuk GA, Aerts R, Freriks S, Röling WFM, van Bodegom PM. Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland. Front Microbiol 2017; 8:317. [PMID: 28326062 PMCID: PMC5339224 DOI: 10.3389/fmicb.2017.00317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/15/2017] [Indexed: 12/21/2022] Open
Abstract
The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.
Collapse
Affiliation(s)
- James T Weedon
- Department of Ecological Science, Vrije Universiteit AmsterdamAmsterdam, Netherlands; Research Group of Plant and Vegetation Ecology, Department of Biology, University of AntwerpAntwerp, Belgium
| | - George A Kowalchuk
- Ecology and Biodiversity, Department of Biology, Utrecht University Utrecht, Netherlands
| | - Rien Aerts
- Department of Ecological Science, Vrije Universiteit Amsterdam Amsterdam, Netherlands
| | - Stef Freriks
- Department of Ecological Science, Vrije Universiteit Amsterdam Amsterdam, Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam Amsterdam, Netherlands
| | - Peter M van Bodegom
- Department of Ecological Science, Vrije Universiteit AmsterdamAmsterdam, Netherlands; Institute of Environmental Sciences, Leiden UniversityLeiden, Netherlands
| |
Collapse
|
45
|
Gang F, Wei S, Shaowei L, Jing Z, Chengqun Y, Zhenxi S. Modeling Aboveground Biomass Using MODIS Images and Climatic Data in Grasslands on the Tibetan Plateau. ACTA ACUST UNITED AC 2017. [DOI: 10.5814/j.issn.1674-764x.2017.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
46
|
Xiong J, Xiong S, Qian P, Zhang D, Liu L, Fei Y. Thermal discharge-created increasing temperatures alter the bacterioplankton composition and functional redundancy. AMB Express 2016; 6:68. [PMID: 27620732 PMCID: PMC5016491 DOI: 10.1186/s13568-016-0238-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/30/2016] [Indexed: 01/07/2023] Open
Abstract
Elevated seawater temperature has altered the coupling between coastal primary production and heterotrophic bacterioplankton respiration. This shift, in turn, could influence the feedback of ocean ecosystem to climate warming. However, little is known about how natural bacterioplankton community responds to increasing seawater temperature. To investigate warming effects on the bacterioplankton community, we collected water samples from temperature gradients (ranged from 15.0 to 18.6 °C) created by a thermal flume of a coal power plant. The results showed that increasing temperatures significantly stimulated bacterial abundance, grazing rate, and altered bacterioplankton community compositions (BCCs). The spatial distribution of bacterioplankton community followed a distance similarity decay relationship, with a turnover of 0.005. A variance partitioning analysis showed that temperature directly constrained 2.01 % variation in BCCs, while temperature-induced changes in water geochemical and grazing rate indirectly accounted for 4.03 and 12.8 % of the community variance, respectively. Furthermore, the relative abundances of 24 bacterial families were linearly increased or decreased (P < 0.05 in all cases) with increasing temperatures. Notably, the change pattern for a given bacterial family was in concert with its known functions. In addition, community functional redundancy consistently decreased along the temperature gradient. This study demonstrates that elevated temperature, combined with substrate supply and trophic interactions, dramatically alters BCCs, concomitant with decreases in functional redundancy. The responses of sensitive assemblages are temperature dependent, which could indicate temperature departures.
Collapse
|
47
|
Zhu C, Ling N, Guo J, Wang M, Guo S, Shen Q. Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil. Front Microbiol 2016; 7:1840. [PMID: 27899920 PMCID: PMC5110519 DOI: 10.3389/fmicb.2016.01840] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/01/2016] [Indexed: 01/13/2023] Open
Abstract
The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on AMF community composition were correlated with organic matter composition in maize rhizosphere soil and the application of manure could activate more AMF species to interact with other species in the maize rhizosphere. This knowledge can be valuable in regulating the symbiotic system of plants and AMF, maintaining the health and high yields of crops and providing a primary basis for rational fertilization.
Collapse
Affiliation(s)
- Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Min Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University Nanjing, China
| |
Collapse
|
48
|
Environmental Humidity Regulates Effects of Experimental Warming on Vegetation Index and Biomass Production in an Alpine Meadow of the Northern Tibet. PLoS One 2016; 11:e0165643. [PMID: 27798690 PMCID: PMC5087907 DOI: 10.1371/journal.pone.0165643] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/14/2016] [Indexed: 11/19/2022] Open
Abstract
Uncertainty about responses of vegetation index, aboveground biomass (AGB) and gross primary production (GPP) limits our ability to predict how climatic warming will influence plant growth in alpine regions. A field warming experiment was conducted in an alpine meadow at a low (4313 m), mid- (4513 m) and high elevation (4693 m) in the Northern Tibet since May 2010. Growing season vapor pressure deficit (VPD), soil temperature (Ts) and air temperature (Ta) decreased with increasing elevation, while growing season precipitation, soil moisture (SM), normalized difference vegetation index (NDVI), soil adjusted vegetation index (SAVI), AGB and GPP increased with increasing elevation. The growing season Ta, Ts and VPD in 2015 was greater than that in 2014, while the growing season precipitation, SM, NDVI, SAVI, AGB and GPP in 2015 was lower than that in 2014, respectively. Compared to the mean air temperature and precipitation during the growing season in 1963–2015, it was a warmer and wetter year in 2014 and a warmer and drier year in 2015. Experimental warming increased growing season Ts, Ta,VPD, but decreased growing season SM in 2014–2015 at all the three elevations. Experimental warming only reduced growing season NDVI, SAVI, AGB and GPP at the low elevation in 2015. Growing season NDVI, SAVI, AGB and GPP increased with increasing SM and precipitation, but decreased with increasing VPD, indicating vegetation index and biomass production increased with environmental humidity. The VPD explained more variation of growing season NDVI, SAVI, AGB and GPP compared to Ts, Ta and SM at all the three elevations. Therefore, environmental humidity regulated the effect of experimental warming on vegetation index and biomass production in alpine meadows on the Tibetan Plateau.
Collapse
|
49
|
Sustained acceleration of soil carbon decomposition observed in a 6-year warming experiment in a warm-temperate forest in southern Japan. Sci Rep 2016; 6:35563. [PMID: 27748424 PMCID: PMC5066277 DOI: 10.1038/srep35563] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/03/2016] [Indexed: 11/09/2022] Open
Abstract
To examine global warming's effect on soil organic carbon (SOC) decomposition in Asian monsoon forests, we conducted a soil warming experiment with a multichannel automated chamber system in a 55-year-old warm-temperate evergreen broadleaved forest in southern Japan. We established three treatments: control chambers for total soil respiration, trenched chambers for heterotrophic respiration (Rh), and warmed trenched chambers to examine warming effect on Rh. The soil was warmed with an infrared heater above each chamber to increase soil temperature at 5 cm depth by about 2.5 °C. The warming treatment lasted from January 2009 to the end of 2014. The annual warming effect on Rh (an increase per °C) ranged from 7.1 to17.8% °C-1. Although the warming effect varied among the years, it averaged 9.4% °C-1 over 6 years, which was close to the value of 10.1 to 10.9% °C-1 that we calculated using the annual temperature-efflux response model of Lloyd and Taylor. The interannual warming effect was positively related to the total precipitation in the summer period, indicating that summer precipitation and the resulting soil moisture level also strongly influenced the soil warming effect in this forest.
Collapse
|
50
|
Zhang K, Shi Y, Jing X, He JS, Sun R, Yang Y, Shade A, Chu H. Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau. Front Microbiol 2016; 7:1032. [PMID: 27446064 PMCID: PMC4927576 DOI: 10.3389/fmicb.2016.01032] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/20/2016] [Indexed: 01/26/2023] Open
Abstract
Soil microbial communities are influenced by climate change drivers such as warming and altered precipitation. These changes create abiotic stresses, including desiccation and nutrient limitation, which act on microbes. However, our understanding of the responses of microbial communities to co-occurring climate change drivers is limited. We surveyed soil bacterial and fungal diversity and composition after a 1-year warming and altered precipitation manipulation in the Tibetan plateau alpine grassland. In isolation, warming and decreased precipitation treatments each had no significant effects on soil bacterial community structure; however, in combination of both treatments altered bacterial community structure (p = 0.03). The main effect of altered precipitation specifically impacted the relative abundances of Bacteroidetes and Gammaproteobacteria compared to the control, while the main effect of warming impacted the relative abundance of Betaproteobacteria. In contrast, the fungal community had no significant response to the treatments after 1-year. Using structural equation modeling (SEM), we found bacterial community composition was positively related to soil moisture. Our results indicate that short-term climate change could cause changes in soil bacterial community through taxonomic shifts. Our work provides new insights into immediate soil microbial responses to short-term stressors acting on an ecosystem that is particularly sensitive to global climate change.
Collapse
Affiliation(s)
- Kaoping Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science Nanjing, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science Nanjing, China
| | - Xin Jing
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University Beijing, China
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking UniversityBeijing, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of SciencesXining, China
| | - Ruibo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science Nanjing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science Nanjing, China
| |
Collapse
|