The Abundance of the nifH Gene Became Higher and the nifH-Containing Diazotrophic Bacterial Communities Changed During Primary Succession in the Hailuogou Glacier Chronosequence, China.
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ABSTRACT:
SUBMITTER: Wang Y
PROVIDER: S-EPMC8200853 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Microbes that produce phosphatases play an important role in the cycling of phosphorus (P), a key nutrient in soil development. We studied the development, compositional turnover, and environmental drivers of microbial communities carrying the phosphatase-encoding phoD gene (here called phoD communities) in the course of primary succession in the Hailuogou glacier chronosequence. We selected the pioneer species Populus purdomii Rehder as a model plant to study the communities in rhizosphere and bulk soils along the chronosequence. The bulk and rhizosphere soils hosted distinct phoD communities. Changes in the taxa Pseudomonas and Pleomorphomonas in the rhizosphere and Bradyrhizobium, Cupriavidus, and Pleomorphomonas in the bulk soil were associated with soil development. The plant development and soil property changes along the chronosequence were accompanied with changes in the phoD communities. Soil pH, soil organic carbon, and total nitrogen contents that are directly related to the plant development and litter input differences along the chronosequence were the main factors related to changes in community compositions. The community similarity decreased along the chronosequence, and the distance decay rate was higher in the bulk soil than in the rhizosphere. In summary, both in the rhizosphere and in bulk soils the phoD community succession was shaped by plant and soil development-related factors along the primary succession in the Hailuogou glacier chronosequence.IMPORTANCE Phosphorus was the key limiting nutrient for soil development during primary succession that occurred in alpine and high-latitude ecosystems with cold and humid climates. The interactions of functional microbiota involved in phosphorus cycling in the rhizosphere under different soil developmental stages along primary succession are still rarely examined. We selected the pioneer species Populus purdomii as a model plant to study the phoD-harboring bacterial communities in rhizosphere and bulk soils along a mountain glacier chronosequence. Our results showed that the bulk soils and rhizosphere host distinct phoD communities and diversity that differentially varied along the chronosequence, describing in detail the development and compositional turnover of the phoD community in the course of primary succession and determining the main environmental factors driving the development.
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Project description:As the two limiting nutrients for plants in most terrestrial ecosystems, nitrogen (N) and phosphorus (P) are essential for the development of succession forests. Vegetation N:P stoichiometry is a useful tool for detecting nutrient limitation. In the present work, chronosequence analysis was employed to research N and P accumulation dynamics and their stoichiometry during forest primary succession in a glacier retreat area on the Tibetan Plateau. Our results showed that: (1) total ecosystem N and P pools increased from 97 kg hm-2 to 7186 kg hm-2 and 25 kg hm-2 to 487 kg hm-2, respectively, with increasing glacier retreat year; (2) the proportion of the organic soil N pool to total ecosystem N sharply increased with increasing glacier retreat year, but the proportion of the organic soil and the vegetation P pools to the total ecosystem P was equivalent after 125 y of recession; (3) the N:P ratio for tree leaves ranged from 10.1 to 14.3, whereas the N:P ratio for total vegetation decreased form 13.3 to 8.4 and remained constant after 35 y of recession, and the N:P ratio for organic soil increased from 0.2 to 23.1 with increasing glacier retreat. These results suggested that organic soil N increased with increasing years of glacier retreat, which may be the main sink for atmospheric N, whereas increased P accumulation in vegetation after 125 y of recession suggested that much of the soil P was transformed into the biomass P pool. As the N:P ratio for vegetation maintained a low level for 35-125 y of recession, we suggested that N might be the main limiting element for plant growth in the development of this ecosystem.
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Project description:Background:The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier's retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods:The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results:nosZ-denitrifiers were more abundant and diverse in soils from successional years 20-60 compared to 0-5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40-60 years) than in younger soils (?20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0-20 years) and in the mature phase (40-60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the community composition of nosZ-denitrifiers (P < 0.05 by Monte Carlo permutation test within RDA analysis).
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Project description:Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The oprJ and mexF genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mexF gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence.
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Project description:We used measurements from airborne imaging spectroscopy and LiDAR to quantify the biophysical structure and composition of vegetation on a dryland substrate age gradient in Hawaii. Both vertical stature and species composition changed during primary succession, and reveal a progressive increase in vertical stature on younger substrates followed by a collapse on Pleistocene-aged flows. Tall-stature Metrosideros polymorpha woodlands dominated on the youngest substrates (hundreds of years), and were replaced by the tall-stature endemic tree species Myoporum sandwicense and Sophora chrysophylla on intermediate-aged flows (thousands of years). The oldest substrates (tens of thousands of years) were dominated by the short-stature native shrub Dodonaea viscosa and endemic grass Eragrostis atropioides. We excavated 18 macroscopic charcoal fragments from Pleistocene-aged substrates. Mean radiocarbon age was 2,002 years and ranged from < 200 to 7,730. Genus identities from four fragments indicate that Osteomeles spp. or M. polymorpha once occupied the Pleistocene-aged substrates, but neither of these species is found there today. These findings indicate the existence of fires before humans are known to have occupied the Hawaiian archipelago, and demonstrate that a collapse in vertical stature is prevalent on the oldest substrates. This work contributes to our understanding of prehistoric fires in shaping the trajectory of primary succession in Hawaiian drylands.
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Project description:Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.
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Project description:Diazotrophs in the mangrove rhizosphere play a major role in providing new nitrogen to the mangrove ecosystem and their composition and activity are strongly influenced by anthropogenic activity and ecological conditions. In this study, the diversity of the diazotroph communities in the rhizosphere sediment of five tropical mangrove sites with different levels of pollution along the north and south coastline of Singapore were studied by pyrosequencing of the nifH gene. Bioinformatics analysis revealed that in all the studied locations, the diazotroph communities comprised mainly of members of the diazotrophic cluster I and cluster III. The detected cluster III diazotrophs, which were composed entirely of sulfate-reducing bacteria, were more abundant in the less polluted locations. The metabolic capacities of these diazotrophs indicate the potential for bioremediation and resiliency of the ecosystem to anthropogenic impact. In heavily polluted locations, the diazotrophic community structures were markedly different and the diversity of species was significantly reduced when compared with those in a pristine location. This, together with the increased abundance of Marinobacterium, which is a bioindicator of pollution, suggests that anthropogenic activity has a negative impact on the genetic diversity of diazotrophs in the mangrove rhizosphere.
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Project description:Succession is defined as changes in biological communities over time. It has been extensively studied in plant communities, but little is known about bacterial succession, in particular in environments such as High Arctic glacier forelands. Bacteria carry out key processes in the development of soil, biogeochemical cycling and facilitating plant colonization. In this study we sampled two roughly parallel chronosequences in the foreland of Midre Lovén glacier on Svalbard, Norway and tested whether any of several factors were associated with changes in the structure of bacterial communities, including time after glacier retreat, horizontal variation caused by the distance between chronosequences and vertical variation at two soil depths. The structures of soil bacterial communities at different locations were compared using terminal restriction fragment length polymorphisms of 16S rRNA genes, and the data were analyzed by sequential analysis of log-linear statistical models. Although no significant differences in community structure were detected between the two chronosequences, statistically significant differences between sampling locations in the surface and mineral soils could be demonstrated even though glacier forelands are patchy and dynamic environments. These findings suggest that bacterial succession occurs in High Arctic glacier forelands but may differ in different soil depths.
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Project description:Arbuscular mycorrhizal (AM) fungi play an important role in plant-fungi communities. It remains a central question of how the AM fungal community changes as plants grow. To establish an understanding of AM fungal community dynamics associated with Chinese fir, Chinese fir with five different growth stages were studied and 60 root samples were collected at the Jiangle National Forestry Farm, Fujian Province. A total of 76 AM fungal operational taxonomic units (OTUs) were identified by high-throughput sequencing on an Illumina Miseq platform. The genera covered by OTUs were Glomus, Archaeospora, Acaulospora, Gigaspora and Diversispora. Glomus dominated the community in the whole stage. The number and composition of OTUs varied along with the host plant growth. The number of OTUs showed an inverted V-shaped change with the host plant age, and the maximum occurred in 23-year. Overall, the basic species diversity and richness in this study were stable. Non-metric multi-dimensional scaling (NMDS) analysis based on bray-curtis distance revealed that there were remarkable differentiations between the 9-year and other stages. Besides, AM fungal community in 32-year had a significant difference with that of 23-year, while no significant difference with that of 45-year, suggesting that 32-year may be a steady stage for AM fungi associated with Chinese fir. The cutting age in 32-year may be the most favorable for microbial community. The pH, total N, total P, total K, available N, available P, available K, organic matter and Mg varied as the Chinese fir grows. According to Mantel test and redundancy analysis, available N, available P, K and Mg could exert significant influence on AM fungal communities, and these variables explained 31% of variance in the composition of AM fungal communities.
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