Soil properties drive microbial community structure in a large scale transect in South Eastern Australia

Soil microbial communities directly affect soil functionality through their roles in the cycling of soil nutrients and carbon storage. Microbial communities vary substantially in space and time, between soil types and under different land management. The mechanisms that control the spatial distributions of soil microbes are largely unknown as we have not been able to adequately upscale a detailed analysis of the microbiome in a few grams of soil to that of a catchment, region or continent. Here we reveal that soil microbes along a 1000 km transect have unique spatial structures that are governed mainly by soil properties. The soil microbial community assessed using Phospholipid Fatty Acids showed a strong gradient along the latitude gradient across New South Wales, Australia. We found that soil properties contributed the most to the microbial distribution, while other environmental factors (e.g., temperature, elevation) showed lesser impact. Agricultural activities reduced the variation of the microbial communities, however, its influence was local and much less than the overall influence of soil properties. The ability to predict the soil and environmental factors that control microbial distribution will allow us to predict how future soil and environmental change will affect the spatial distribution of microbes

Patterns in soil microbial diversity across Europe.

Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia.

BACKGROUND: The human intestine and its microbiota is the most common infection site for soil-transmitted helminths (STHs), which affect the well-being of ~ 1.5 billion people worldwide. The complex cross-kingdom interactions are not well understood. RESULTS: A cross-sectional analysis identified conserved microbial signatures positively or negatively associated with STH infections across Liberia and Indonesia, and longitudinal samples analysis from a double-blind randomized trial showed that the gut microbiota responds to deworming but does not transition closer to the uninfected state. The microbiomes of individuals able to self-clear the infection had more alike microbiome assemblages compared to individuals who remained infected. One bacterial taxon (Lachnospiracae) was negatively associated with infection in both countries, and 12 bacterial taxa were significantly associated with STH infection in both countries, including Olsenella (associated with reduced gut inflammation), which also significantly reduced in abundance following clearance of infection. Microbial community gene abundances were also affected by deworming. Functional categories identified as associated with STH infection included arachidonic acid metabolism; arachidonic acid is the precursor for pro-inflammatory leukotrienes that threaten helminth survival, and our findings suggest that some modulation of arachidonic acid activity in the STH-infected gut may occur through the increase of arachidonic acid metabolizing bacteria. CONCLUSIONS: For the first time, we identify specific members of the gut microbiome that discriminate between moderately/heavily STH-infected and non-infected states across very diverse geographical regions using two different statistical methods. We also identify microbiome-encoded biological functions associated with the STH infections, which are associated potentially with STH survival strategies, and changes in the host environment. These results provide a novel insight of the cross-kingdom interactions in the human gut ecosystem by unlocking the microbiome assemblages at taxonomic, genetic, and functional levels so that advances towards key mechanistic studies can be made. Microbiome 2018 Feb 28; 6(1):33

Soil Microbial Diversity Across Different Agroecological Zones in New South Wales

A synergistic relationship between soil diversity (pedodiversity) and soil microbial diversity (biodiversity) seems axiomatic. Soil microbes contribute with biogeochemical cycles on which rely soil services (e.g. food production) and; vice-versa the soil matrix provides the living conditions that structure its microbial communities. A better insight would enable us to quantify/qualify and so sustain, protect, and improve those processes underpinned by soil microorganisms. We hypothesize that the structural patterns of soil microbes rely on multivariate soil units and gradients (e.g. soil horizons) instead of single discrete ‘factors’ (soil pH) and that the microbial patterns can become a well-defined property of determined soils. We began exploring this biotic-abiotic dynamic by modeling soil microbial α-diversity using two orthogonal transects (~900 km each) across NSW. Soils were sampled from paired conserved and disturbed ecosystems. Soil biophysicochemistry was characterized using 16SrDNA/ITS metabarcoding and pedometric approaches. Soil microbial patterns and physicochemical attributes were assessed using linear and non-linear relationships (bootstraped regression trees models) whose output enabled the microbial mapping at 1km across NSW. These maps showed a higher diversity of soil microbes in western than eastern NSW. Despite this gradient, fungi and archaea were respectively lower and higher in Vertosols, whereas bacteria distribution was less clear. Our results suggested that microbial structural patterns relate to most pedological attributes and, the extent of this relationship varies according to the structural parameters analyzed (taxa composition, abundance, diversity metric). Therefore, microbial patterns are more consistent with grouped features defining soil gradients (soil types) rather than on individual soil properties. These conclusions will be supported by analyzing microbial and pedological dissimilarities (β-diversity) in a further research

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

To better understand the relationship between soil bacterial communities, soil physicochemical properties, land use and geographical distance, we considered for the first time ever a European transect running from Sweden down to Portugal and from France to Slovenia. We investigated 71 sites based on their range of variation in soil properties (pH, texture and organic matter), climatic conditions (Atlantic, alpine, boreal, continental, Mediterranean) and land uses (arable, forest and grassland). 16S rRNA gene amplicon pyrosequencing revealed that bacterial communities highly varied in diversity, richness, and structure according to environmental factors. At the European scale, taxa area relationship (TAR) was significant, supporting spatial structuration of bacterial communities. Spatial variations in community diversity and structure were mainly driven by soil physicochemical parameters. Within soil clusters (k-means approach) corresponding to similar edaphic and climatic properties, but to multiple land uses, land use was a major driver of the bacterial communities. Our analyses identified specific indicators of land use (arable, forest, grasslands) or soil conditions (pH, organic C, texture). These findings provide unprecedented information on soil bacterial communities at the European scale and on the drivers involved; possible applications for sustainable soil management are discussed

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.Peer reviewe

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms

Innovative Spent Coffee Ground-Based Biofertilizer: Effects on Soil Microbiome and Crop Health

Aim: Crop health is strictly related to soil biodiversity. The transition from chemical fertilizers to biofertilizers may represent a sustainable way to restore soil biodiversity, improve crop health and productivity. Spent coffee ground (SCG) is a waste material with a high potential for the development of innovative biofertilizers. However, previous research showed that the use of SCG as fertilizer inhibits plants growth, mainly due to the presence of phytotoxic compounds. On the contrary, SCG-treated plants showed high nutritional values with an increased content in antioxidants and mineral elements. The aim of this research was to test the effects of an innovative SCG-based biofertilizer (BF) on salad crops (Lactuca sativa), and on their rhizosphere microbial communities. And thus, to evaluate its potential in mitigating SCG’s negative effects. Method: A randomized block design experiment was carried to compare the effects of BF and SCG at 3 different concentrations, each with 5 replicates. Plants functional traits and nutritional values were evaluated. 16S rRNA gene metabarcoding was used to assess the effects on rhizosphere communities. Results: BF-treated plants showed a higher polyphenols level and less stress signs compared to the SCG-treated and control ones. At the highest concentrations, BF modify bacterial communities with an increase of plant growth-promoting rhizobacteria (e.g., Azospirillium, Arachidicoccus) and other beneficial bacterial taxa, such as those involved in disease suppression, aromatic compounds degradation, nutrients cycling. Conclusions: BF resulted capable of reducing SCG negative effects on plant health, promoting the growth of plants beneficial microbial taxa and, therefore, favouring a healthier growth of crops

Influence of Organic and Conventional Management Systems on Soil Microarthropods in Protected and Non-Protected Areas

Aim: The EU Biodiversity Strategy 2030 aims to increase land-protected areas at 30% and organic farming at 25% of agricultural lands. But which measure could be more effective in preserving soil biodiversity? The aim of the study is, therefore, to assess soil health of arable lands under organic and conventional managements in Non-protected (NPAorg) and Protected (PAcon) areas of Marche region (Italy) and compare the influence of the applied farming practices on soil microarthropods in two seasons, characterized by different intensities of soil management practices: spring (lower) and autumn (higher). Method: Soil health has been assessed through the Biological Quality of Soil index based on arthropods (QBS-ar). Novel approaches (QBS-ab and FAI indices) which consider microarthropods’ abundance in the index calculation, have been also applied. Density (ind/m2), Acari/Collembola ratio, % of Oribatid mites on total mites, biodiversity indices, correlations with chemical-physical parameters, and ordination analysis (nMDS) have been evaluated. Results: In both seasons, different communities have been found according to management and, particularly, PAcon sites showed significantly higher levels of biodiversity compared to NPAorg. However, in autumn, microarthropod communities present higher stability in NPAorg sites, showing an opposite trend and fewer fluctuations of the indices compared to PAcon. Conclusions: PA, even in conventional managed soils, seem to enhance soil biodiversity, while organic farming in NPA, confers a higher resilience to soil, making microarthropod communities more stable. Results showed that agricultural intensity reduction combined with the increased integration of agroecosystems in protected areas may represent an effective, and sustainable measure to preserve soil biodiversity and its ecological services