Elevation-related climatic factors dominate soil free-living nematode communities and their co-occurrence patterns on Mt. Halla, South Korea.
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ABSTRACT: Nematodes play vital roles in soil ecosystems. To understand how their communities and coexistence patterns change along the elevation as well as to determine the best explanatory factors underlying these changes, we investigated free-living soil nematodes on Mt. Halla, South Korea, using an amplicon sequencing approach targeting the 18S rRNA gene. Our results showed that there was significant variation in the community diversity and composition of soil nematodes in relation to elevation. The network interactions between soil nematodes were more intensive at the lower elevations. Climatic variables were responsible explaining the elevational variation in community composition and co-occurrence pattern of the nematode community. Our study indicated that climatic factors served as the critical environmental filter that influenced not only the community structure but also the potential associations of soil nematodes in the mountain ecosystem of Mt. Halla. These findings enhance the understanding of the community structure and co-occurrence network patterns and mechanisms of soil nematode along elevation, and the response of soil nematodes to climate change on the vertical scale of mountain ecosystems.
Project description:To improve our understanding of the relationship between soil higher fungi (belonging to Ascomycota and Basidiomycota) and Abies koreana, we surveyed A. koreana soil fungal communities in a forest in Mt. Halla, Jeju Island, Korea by next-generation sequencing (Illumina Miseq). To confirm the soil higher fungal communities, we collected two types of soils from a defined plot: soils with dead (AKDTs) and living A. koreana (AKLTs), respectively. Soil fungi were classified into 2 phyla, 19 classes, 64 orders, 133 families, 195 genera, and 229 OTUs (895,705 sequence reads). Nonmetric multidimensional scaling (NMDS) showed significantly different soil higher fungal communities between AKDTs and AKLTs (p < .05). In addition, the saprophyte composition was significantly affected by A. koreana status (p < .05). The proportion of the mycorrhizal Clavulina spp. was different between soils with AKDTs and AKLTs, suggesting that Clavulina spp. may be a crucial soil fungal species influencing A. koreana. This study will lead to a better understanding of the ecological status of A. koreana in Mt. Halla. In addition, this study could be useful for the conservation and management of A. koreana habitats.
Project description:Periglacial soils are one of the least studied ecosystems on Earth, yet they are widespread and are increasing in area due to retreat of glaciers worldwide. Soils in these environments are cold and during the brief summer are exposed to high levels of UV radiation and dramatic fluctuations in moisture and temperature. Recent research suggests that these environments harbor immense microbial diversity. Here we use sequencing of environmental DNA, culturing of isolates, and analysis of environmental variables to show that members of the Chytridiomycota (chytrids) dominate fungal biodiversity and perhaps decomposition processes in plant-free, high-elevation soils from the highest mountain ranges on Earth. The zoosporic reproduction of chytrids requires free water, yet we found that chytrids constituted over 70% of the ribosomal gene sequences of clone libraries from barren soils of the Himalayas and Rockies; by contrast, they are rare in other soil environments. Very few chytrids have been cultured, although we were successful at culturing chytrids from high-elevation sites throughout the world. In a more focused study of our sites in Colorado, we show that carbon sources that support chytrid growth (eolian deposited pollen and microbial phototrophs) are abundant and that soils are saturated with water for several months under the snow, thus creating ideal conditions for the development of a chytrid-dominated ecosystem. Our work broadens the known biodiversity of the Chytridomycota, and describes previously unsuspected links between aquatic and terrestrial ecosystems in alpine regions.
Project description:Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide.
Project description:The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.
Project description:This study investigated the development of fungal community composition in arable soil during the degradation of straw residue. We explored the short-term responses of the fungal community over 28 days of decomposition in soil using culture-independent polymerase chain reaction in combination with a clone library and denaturing gradient gel electrophoresis (DGGE). Fungal cellobiohydrolase I (cbhI) genes in the soil were also characterized, and their diversity suggested the existence of a different cellulose decomposer. The DGGE profiles based on fungal internal transcribed spacer analysis showed different successions of fungal populations during residue decomposition. Members of Lecythophora and Sordariales were dominant in the early succession, while Hypocrea and Engyodontium were better adapted in the late succession. The succession of fungal communities might be related to changes of residue quality during decomposition. Collectively, sequences assigned to Ascomycota members were dominant at different stages of the fungal succession during decomposition, revealing that they were key drivers responsible for residue degradation in the arable soil tested.
Project description:BackgroundElevation trends of macro organisms have long been well studied. However, whether microbes also exhibit such patterns of elevation change is unknown. Here, we investigated the changes in bamboo forest soil bacterial communities along six elevation gradients, from 600 to 1800 m a.s.l. in Mt. Da-an, a subtropical montane area in Nantou county at central Taiwan.ResultsData from 16S rRNA gene clone libraries revealed that more than 70 % of the six communities contained Acidobacteria and Proteobacteria, although the relative abundance differed. Nonmetric multidimensional scaling analysis of the distribution of operational taxonomic units showed differences in bamboo soil bacterial communities across gradients. The bacterial communities at 1000 and 1200 m showed greater diversity than the communities at both lower (600 and 800 m) and higher (1400 and 1800 m) elevations. In contrast to the bacterial community trend, soil C and N and microbial biomass properties increased linearly with elevation.ConclusionThe bamboo soil bacterial community could interact with multiple factors such as soil organic matter content and temperature, for differences in composition and diversity with change in elevation.
Project description:To study the soil mcirobial functional communities and the nutrient cycles couplings changes after exposure to different contaminant
Project description:Little is known about how nematode ecology differs across elevational gradients. We investigated the soil nematode community along a ~2,200 m elevational range on Mt. Norikura, Japan, by sequencing the 18S rRNA gene. As with many other groups of organisms, nematode diversity showed a high correlation with elevation, and a maximum in mid-elevations. While elevation itself, in the context of the mid domain effect, could predict the observed unimodal pattern of soil nematode communities along the elevational gradient, mean annual temperature and soil total nitrogen concentration were the best predictors of diversity. We also found nematode community composition showed strong elevational zonation, indicating that a high degree of ecological specialization that may exist in nematodes in relation to elevation-related environmental gradients and certain nematode OTUs had ranges extending across all elevations, and these generalized OTUs made up a greater proportion of the community at high elevations - such that high elevation nematode OTUs had broader elevational ranges on average, providing an example consistent to Rapoport's elevational hypothesis. This study reveals the potential for using sequencing methods to investigate elevational gradients of small soil organisms, providing a method for rapid investigation of patterns without specialized knowledge in taxonomic identification.
Project description:Variable climatic conditions strongly influence phytoplankton dynamics in estuaries globally. Our study area is Chesapeake Bay, a highly productive ecosystem providing natural resources, transportation, and recreation for nearly 16 million people inhabiting a 165,000-km(2) watershed. Since World War II, nutrient over-enrichment has led to multiple ecosystem impairments caused by increased phytoplankton biomass as chlorophyll-a (chl-a). Doubled nitrogen (N) loadings from 1945-1980 led to increased chl-a, reduced water clarity, and low dissolved oxygen (DO), while decreased N loadings from 1981-2012 suggest modest improvement. The recent 30+ years are characterized by high inter-annual variability of chl-a, coinciding with irregular dry and wet periods, complicating the detection of long-term trends. Here, we synthesize time-series data for historical and recent N loadings (TN, NO2 + NO3), chl-a, floral composition, and net primary productivity (NPP) to distinguish secular changes caused by nutrient over-enrichment from spatio-temporal variability imposed by climatic conditions. Wet years showed higher chl-a, higher diatom abundance, and increased NPP, while dry years showed lower chl-a, lower diatom abundance, and decreased NPP. Our findings support a conceptual model wherein variable climatic conditions dominate recent phytoplankton dynamics against a backdrop of nutrient over-enrichment, emphasizing the need to separate these effects to gauge progress toward improving water quality in estuaries.