ORCID Profile
0000-0002-2364-9908
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Publisher: Springer Science and Business Media LLC
Date: 06-01-2023
DOI: 10.1007/S10980-022-01572-Z
Abstract: Human-induced changes in landscape structure are among the main causes of bio ersity loss. Despite their important contribution to bio ersity and ecosystem functioning, microbes—and particularly protists—remain spatially understudied. Soil microbiota are most often driven by local soil properties, but the influence of the surrounding landscape is rarely assessed. We assessed the effect of landscape structure on soil protist alpha and beta ersity in meadows in the western Swiss Alps. We s led 178 plots along an elevation gradient representing a broad range of environmental conditions and land-use. We measured landscape structure around each plot at 5 successive spatial scales (i.e. neighbourhood windows of increasing radius, ranging from 100 to 2000 m around a plot). We investigated the changes of protist alpha and beta ersity as a function of landscape structure, local environmental conditions and geographic distance. Landscape structures, especially percentage of meadows, forests, or open habitats, played a key role for protist alpha and beta ersity. The importance of landscape structure was comparable to that of environmental conditions and spatial variables, and increased with the size of the neighbourhood window considered. Our results suggest that dispersal from neighbouring habitats is a key driver of protist alpha and beta ersity which highlight the importance of landscape-scale assembly mechanisms for microbial ersity. Landscape structure emerges as a key driver of microbial communities which has profound implications for our understanding of the consequences of land-use change on soil microbial communities and their associated functions.
Publisher: Springer Science and Business Media LLC
Date: 12-03-2021
DOI: 10.1038/S41396-021-00947-5
Abstract: Soil bacteria are largely missing from future bio ersity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for ex le on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and ersity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.
Publisher: Cold Spring Harbor Laboratory
Date: 13-04-2022
DOI: 10.1101/2022.04.13.488160
Abstract: Human-induced changes in landscape structure are among the main causes of bio ersity loss. Despite their important contribution to bio ersity and ecosystem functioning, microbes - and particularly protists - remain spatially understudied. Soil microbiota are most often driven by local soil properties, but the influence of the surrounding landscape is rarely assessed. We assessed the effect of landscape structure on soil protist alpha and beta ersity in meadows in the western Swiss Alps. We s led 178 plots along an elevation gradient representing a broad range of environmental conditions and land-use. We measured landscape structure around each plot at 5 successive spatial scales (i.e. neighbourhood windows of increasing radius, ranging from 100 to 2000 m around a plot). We investigated the changes of protist alpha and beta ersity as a function of landscape structure, local environmental conditions and geographic distance. Landscape structures played a key role for protist alpha and beta ersity. The percentage of meadows, forests, or open habitats had the highest influence among all landscape metrics. The importance of landscape structure was comparable to that of environmental conditions and spatial variables, and increased with the size of the neighbourhood window considered. Our results suggest that dispersal from neighbouring habitats is a key driver of protist alpha and beta ersity which highlight the importance of landscape-scale assembly mechanisms for microbial ersity. Landscape structure emerges as a key driver of microbial communities which has profound implications for our understanding of the consequences of land-use change on soil microbial communities and their associated functions.
Publisher: Elsevier BV
Date: 06-2022
Publisher: American Society for Microbiology
Date: 27-10-2020
Abstract: High-throughput 16S rRNA gene licon sequencing is an essential method for studying the ersity and dynamics of microbial communities. However, this method is presently h ered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene licon sequence variant (FL-ASV) resolved reference databases that include high-identity references ( .
Publisher: Elsevier BV
Date: 03-2021
Publisher: Cold Spring Harbor Laboratory
Date: 18-06-2019
DOI: 10.1101/672873
Abstract: High-throughput 16S rRNA gene licon sequencing is an essential method for studying the ersity and dynamics of microbial communities. However, this method is presently h ered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases, and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here we demonstrate how high-throughput synthetic long-read sequencing can be applied to create ecosystem-specific full-length 16S rRNA gene licon sequence variant (FL-ASV) reference databases that include high-identity references ( .7% identity) for nearly all abundant bacteria ( .01% relative abundance) using Danish wastewater treatment systems and anaerobic digesters as an ex le. In addition, we introduce a novel sequence identity-based approach for automated taxonomy assignment (AutoTax) that provides a complete seven-rank taxonomy for all reference sequences, using the SILVA taxonomy as a backbone, with stable placeholder names for unclassified taxa. The FL-ASVs are perfectly suited for the evaluation of taxonomic resolution and bias associated with primers commonly used for licon sequencing, allowing researchers to choose those that are ideal for their ecosystem. The AutoTax taxonomy greatly improves the classification of short-read 16S rRNA gene licon sequence variants (ASVs) at the genus- and species-level, compared to the commonly used universal reference databases. Importantly, the placeholder names provide a way to explore the unclassified environmental taxa at different taxonomic ranks, which in combination with in situ analyses can be used to uncover their ecological roles.
Publisher: Cold Spring Harbor Laboratory
Date: 05-07-2021
DOI: 10.1101/2021.07.04.450854
Abstract: It is becoming increasingly clear that microbial symbionts influence key aspects of their host’s fitness, and vice versa . This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome ersity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome ersity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was lified in these lines to investigate microbial ersity. We found that 1) host population bottlenecks constrained microbiome richness and ersity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome ersity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial ersity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current bio ersity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial ersity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations. It is becoming increasingly clear that organisms and the microbes that live on or in them – their microbiome – affect each other in profound ways that we are just beginning to understand. For instance, a erse microbiome can help maintain metabolic functions or fight pathogens causing diseases. A disrupted microbiome may be especially critical for animals and plants that occur in low numbers because of threats from e.g. human exploitation or climate change, as they may already suffer from genetic challenges such as inbreeding and reduced evolutionary potential. The importance of such a reduction in population size, called a bottleneck, on the microbial ersity and the potential interactive effects on host health remains unexplored. Here we experimentally test these associations by investigating the microbiomes of 50 inbred or non-inbred populations of vinegar flies. We found that restricting the population size constrain the host’s genetic variation and simultaneously decreases the ersity of the microbiome that they harbor, and that both effects were detrimental to host fitness. The microbial communities in inbred host populations were less robust than in their non-inbred counterparts, suggesting that we should increasingly consider the microbiome ersity, which may ultimately influence the health and persistence of threatened species.
Location: France
Location: United States of America
No related grants have been discovered for Erika Yashiro.