Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach

Effects of riparian pioneer plants on soil aggregate stability: Roles of root traits and rhizosphere microorganisms

Pioneer plants are vital in stabilizing soil structure while restoring reservoir drawdown areas. However, uncertainties persist regarding the mechanism of pioneer plants to soil stability in these delicate ecosystems. This study aims to unravel the plant-soil feedback mechanisms from the roles of root traits and rhizosphere microorganisms. We conducted a mesocosm experiment focusing on four common pioneer plants from the drawdown area of Three Gorges Reservoir, China. Using the wet sieving methodology, trait-based approach and high-throughput sequencing technology, we explored soil aggregate stability parameters, plant root traits and rhizosphere microbial communities in experimental plant groups. The interacting effect of pioneer plant species richness, root traits, and rhizosphere microbial communities on soil aggregate stability was quantified by statistical and machine-learning models. Our results demonstrate that diverse pioneer plant communities significantly enhance soil aggregate stability. Notably, specific species, such as Cynodon dactylon (L.) Pers. and Xanthium strumarium L., exert a remarkably strong influence on soil stability due to their distinctive root traits. Root length density (RLD) and root specific surface area (RSA) were identified as crucial root traits mediating the impact of plant diversity on soil aggregate stability. Additionally, our study highlights the link between increased rhizosphere fungal richness, accompanied by plant species richness, and enhanced soil aggregate stability, likely attributable to elevated RLD and RSA. These insights deepen our understanding of the role of pioneer vegetation in soil structure and stability, providing valuable implications for ecological restoration and management practices in reservoir drawdown areas.

Responses of rhizosphere microbial community structure and metabolic function to heavy metal coinhibition

Metal mineral mining results in releases of large amounts of heavy metals into the environment, and it is necessary to better understand the response of rhizosphere microbial communities to simultaneous stress from multiple heavy metals (HMs), which directly impacts plant growth and human health. In this study, by adding different concentrations of cadmium (Cd) to a soil with high background concentrations of vanadium (V) and chromium (Cr), the growth of maize during the jointing stage was explored under limiting conditions. High-throughput sequencing was used to explore the response and survival strategies of rhizosphere soil microbial communities to complex HM stress. The results showed that complex HMs inhibited the growth of maize at the jointing stage, and the diversity and abundance of maize rhizosphere soil microorganisms were significantly different at different metal enrichment levels. In addition, according to the different stress levels, the maize rhizosphere attracted many tolerant colonizing bacteria, and cooccurrence network analysis showed that these bacteria interacted very closely. The effects of residual heavy metals on beneficial microorganisms (such as Xanthomonas, Sphingomonas, and lysozyme) were significantly stronger than those of bioavailable metals and soil physical and chemical properties. PICRUSt analysis revealed that the different forms of V and Cd had significantly greater effects on microbial metabolic pathways than all forms of Cr. Cr mainly affected the two major metabolic pathways: microbial cell growth and division and environmental information transmission. In addition, significant differences in rhizosphere microbial metabolism under different concentrations were found, and this can serve as a reference for subsequent metagenomic analysis. This study is helpful for exploring the threshold for the growth of crops in toxic HM soils in mining areas and achieving further biological remediation.

Root-associated fungal communities are influenced more by soils than by plant-host root traits in a Chinese tropical forest

Forest fungal communities are shaped by the interactions between host tree root systems and the associated soil conditions. We investigated how the soil environment, root morphological traits, and root chemistry influence root-inhabiting fungal communities in three tropical forest sites of varying successional status in Xishuangbanna, China. For 150 trees of 66 species, we measured root morphology and tissue chemistry. Tree species identity was confirmed by sequencing rbcL, and root-associated fungal (RAF) communities were determined using high-throughput ITS2 sequencing. Using distance-based redundancy analysis and hierarchical variation partitioning, we quantified the relative importance of two soil variables (site average total phosphorus and available phosphorus), four root traits (dry matter content, tissue density, specific tip abundance, and forks), and three root tissue elemental concentrations (nitrogen, calcium, and manganese) on RAF community dissimilarity. The root and soil environment collectively explained 23% of RAF compositional variation. Soil phosphorus explained 76% of that variation. Twenty fungal taxa differentiated RAF communities among the three sites. Soil phosphorus most strongly affects RAF assemblages in this tropical forest. Variation in root calcium and manganese concentrations and root morphology among tree hosts, principally an architectural trade-off between dense, highly branched vs less-dense, herringbone-type root systems, are important secondary determinants.

Impact of land use and land cover change on land degradation in rural semi-arid South Africa: case of the Greater Sekhukhune District Municipality

In semi-arid regions, interactions between biophysical and socio-economic variables are complex. Such interactions and their respective variables significantly alter land use and land cover, degrade landscape's structure, and impede the efficacy of the adopted land management interventions. This scenario is particularly prevalent in communal land tenure system or areas managed by a hybrid of traditional and state led institutions. Hence, this study sought to investigate the impacts of land use and land cover changes (LULCCs) on land degradation (LD) under communal rural districts, and the key drivers of habitat fragmentation in the Greater Sekhukhune District Municipality (GSDM), South Africa. The study used the wet and dry season multi-temporal remotely sensed image data, key-informant interviews, and workshop with tribal council to determine the major drivers of LULCC and LD. Results revealed that mines and quarries, subsistence and commercial cultivation, and thicket/dense bush LULCs declined significantly during the study period. These LULCs mostly declined in wet season, with loss in vegetation cover highly prevalent. Specifically, the highest conversions were from shrub/grassland to bare soil, thicket/dense bush to shrub/grassland, and shrub/grassland to residential, respectively. Generally, LULCC affected vegetation productivity within the study area, with increased negative NDVI values observed during the dry season. The findings from key informants and the tribal council workshop emphasized that soil erosion, abandonment of cropland, and injudicious land use (i.e. overgrazing and consequent bush encroachment) have severely degraded the land. The study also established that the degrading land can be attributed to the weakening local communal land management system, particularly the weakening tribal councils. The study recommends an urgent need for collaborative (i.e. government, tribal authorities, and land users) land management through designing relevant multi-stakeholder LD mitigation measures.

Exploration of pristine plate-tectonic plains and mining exposure areas for indigenous microbial communities and its impact on the mineral-microbial geochemical weathering process in ultramafic setting

Heavy metal release from harsh ultramafic settings influences microbial diversity and function in soil ecology. This study aimed to determine how serpentine mineralosphere bacterial assemblies and their functions differed in two different plate-tectonic plains and mining exposure sites under heavy metal release conditions. The results showed that the Proteobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Chloroflexi were the most abundant bacterial groups among all the sites. The log10-based LDA scores highlighted that some specific groups of bacterial assemblies were enriched in plate-tectonic plains and mining activity areas of the serpentine mineralosphere. Functional prediction revealed that the abundance of heavy metal (Cr and Ni) resistance and biogeochemical cycles involving functional KEGG orthology varied in samples from plate-tectonic plains and mining activity sites. The bipartite plot showed that the enrichment of the biogeochemical cycle and heavy metal resistance functional genes correlated with the abundance of serpentine mineralosphere bacterial groups at a 0.005% confidence level. The co-occurrence network plot revealed that the interconnection pattern of the indigenous bacterial assemblies changed in different plate-tectonic plains and mining exposure areas. Finally, this study concluded that due to heavy metal release, the variation in bacterial assemblies, their functioning, and intercommunity co-occurrence patterns were clarified the synergetic effect of mineral-microbial geochemical weathering process in serpentine mining areas.

Geochemistry and microbiology of tropical serpentine soils in the Santa Elena Ophiolite, a landscape-biogeographical approach

The Santa Elena Ophiolite is a well-studied ultramafic system in Costa Rica mainly comprised of peridotites. Here, tropical climatic conditions promote active laterite formation processes, but the biogeochemistry of the resulting serpentine soils is still poorly understood. The aim of this study was to characterize the soil geochemical composition and microbial community of contrasting landscapes in the area, as the foundation to start exploring the biogeochemistry of metals occurring there. The soils were confirmed as Ni-rich serpentine soils but differed depending on their geographical location within the ophiolite area, showing three serpentine soil types. Weathering processes resulted in mountain soils rich in trace metals such as cobalt, manganese and nickel. The lowlands showed geochemical variations despite sharing similar landscapes: the inner ophiolite lowland soils were more like the surrounding mountain soils rather than the north lowland soils at the border of the ophiolite area, and within the same riparian basin, concentrations of trace metals were higher downstream towards the mangrove area. Microbial community composition reflected the differences in geochemical composition of soils and revealed potential geomicrobiological inputs to local metal biogeochemistry: iron redox cycling bacteria were more abundant in the mountain soils, while more manganese-oxidizing bacteria were found in the lowlands, with the highest relative abundance in the mangrove areas. The fundamental ecological associations recorded in the serpentine soils of the Santa Elena Peninsula, and its potential as a serpentinization endemism hotspot, demonstrate that is a model site to study the biogeochemistry, geomicrobiology and ecology of tropical serpentine areas.

Responses of soil fungal communities and functional guilds to ~160 years of natural revegetation in the Loess Plateau of China

Natural revegetation has been widely confirmed to be an effective strategy for the restoration of degraded lands, particularly in terms of rehabilitating ecosystem productivity and soil nutrients. Yet the mechanisms of how natural revegetation influences the variabilities and drivers of soil residing fungal communities, and its downstream effects on ecosystem nutrient cycling are not well understood. For this study, we investigated changes in soil fungal communities along with ~160 years of natural revegetation in the Loess Plateau of China, employing Illumina MiSeq DNA sequencing analyses. Our results revealed that the soil fungal abundance was greatly enhanced during the later stages of revegetation. As revegetation progresses, soil fungal richness appeared first to rise and then decline at the climax Quercus liaotungensis forest stage. The fungal Shannon and Simpson diversity indexes were the lowest and highest at the climax forest stage among revegetation stages, respectively. Principal component analysis, Bray–Curtis similarity indices, and FUNGuild function prediction suggested that the composition, trophic modes, and functional groups for soil fungal communities gradually shifted along with natural revegetation. Specifically, the relative abundances of Basidiomycota, Agaricomycetes, Eurotiomycetes, and ectomycorrhizal fungi progressively increased, while that of Ascomycota, Sordariomycetes, Dothideomycetes, Tremellomycetes, saprotrophic, pathotrophic, arbuscular mycorrhizal fungi, and endophyte fungi gradually decreased along with natural revegetation, respectively. The most enriched members of Basidiomycota (e.g., Agaricomycetes, Agaricales, Cortinariaceae, Cortinarius, Sebacinales, Sebacinaceae, Tricholomataceae, Tricholoma, Russulales, and Russulaceae) were found at the climax forest stage. As important carbon (C) sources, the most enriched symbiotic fungi (particularly ectomycorrhizal fungi containing more recalcitrant compounds) can promote organic C and nitrogen (N) accumulation in soils of climax forest. However, the most abundant of saprotrophic fungi in the early stages of revegetation decreased soil organic C and N accumulation by expediting the decomposition of soil organic matter. Our results suggest that natural revegetation can effectively restore soil fungal abundance, and modify soil fungal diversity, community composition, trophic modes, and functional groups by altering plant properties (e.g., plant species richness, diversity, evenness, litter quantity and quality), quantity and quality of soil nutrient substrates, soil moisture and pH. These changes in soil fungal communities, particularly their trophic modes and functional groups along with natural revegetation, impact the accumulation and decomposition of soil C and N and potentially affect ecosystem C and N cycling in the Loess Plateau of China.

Living and Dead Microorganisms in Mediating Soil Carbon Stocks Under Long-Term Fertilization in a Rice-Wheat Rotation

Although soil microorganism is an active area of research, we are still in the early stages of understanding how living microorganisms influence the accumulations of soil microbial residues under different agricultural practices. Based on a 39-year fertilization experiment, we characterized the soil microbiota and correlated their compositions to soil microbial residues, which are indicated by amino sugars under a rice-wheat rotation. In the present study, fertilization regimes and crop season all exerted significant impacts on the compositions of soil microbial communities and their residues, although no significant difference in the microbial residues was found between soil depth (0-10 cm vs. 10-20 cm). Compared within fertilization regimes, the long-term fertilization, especially the application of organic manure, stimulated the accumulations of carbon (C) and nitrogen in soils and microbial residues. Upland soils in wheat season accumulated more microbial residues, particularly in fungal residues, than paddy soils in rice season. Our results suggested that the long-term application of organic manure favored the growth of soil microbial communities, and then increased the contents of microbial residues, particularly in fungal residues, leading to an enlargement of soil C pools. The keystone taxa Pseudaleuria identified by network analysis showed a significantly positive potential in soil C sequestration by increasing the accumulation of fungal residues. Thus, this study revealed the strong and close connections between microbial communities and their residues, and provided evidence about the critical role of keystone taxa in regulating C sequestration.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale

Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand.

The response of bacterial communities to V and Cr and novel reducing bacteria near a vanadium‑titanium magnetite refinery

Soil contamination with multiple heavy metals has always been a pressing issue, but little attention has been given to V and Cr and their chemical fractions' impacts on microorganisms because Cr₂O₃ usually occurs as an associated mineral in vanadium mines. To investigate this issue, samples (N1-N6) less affected by anthropogenic activities were selected for microbial analysis. The area near the refinery was heavily contaminated according to the PLI (pollution load index). Actinobacteriota, Proteobacteria, and Chloroflexi were the dominant phyla in the soil. The diversity of bacteria was positively influenced by V and Cr and negatively influenced by pH, while the abundance was positively correlated with soil nutrients. Interestingly, the influence of heavy metals in the residual fraction on the microbial community structure and functional metabolism was higher than that in the oxidizable fraction, which may be due to the relatively low heavy metal valence of the oxidizable fraction, suggesting that low valence binding forms of multivalence elements have little effect on microorganisms in the soil. Ultimately, two strains with great efficiency in reducing V and Cr were screened, and co-occurrence network characteristics with significant positive interactions suggested that Bacillus can coordinate community structure in the same niche. This research will help to explore the bioavailability of heavy metals and further achieve the bioremediation of heavy metal contamination in soil.

Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C4 grassland soils

Background

Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C₄ perennial grasses in nutrient-poor grasslands are not well studied.

Methods

In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha⁻¹) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C₄ grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes.

Results

Nitrosospira were dominant AOB in the C₄ grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C₄ grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N₂O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N₂O emission were significantly related to the variability in AOB community structures (p < 0.05).

Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress

Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.

Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome

Background: There is growing interest in the connection between the gut microbiome and human health and disease. Conventional approaches to analyse microbiome data typically entail dimensionality reduction and assume linearity of the observed relationships, however, the microbiome is a highly complex ecosystem marked by non-linear relationships. In this study, we use topological data analysis (TDA) to explore differences and similarities between the gut microbiome across several countries. Methods: We used curated adult microbiome data at the genus level from the GMrepo database. The dataset contains OTU and demographical data of over 4,400 samples from 19 studies, spanning 12 countries. We analysed the data with tmap, an integrative framework for TDA specifically designed for stratification and enrichment analysis of population-based gut microbiome datasets. Results: We find associations between specific microbial genera and groups of countries. Specifically, both the USA and UK were significantly co-enriched with the proinflammatory genera Lachnoclostridium and Ruminiclostridium, while France and New Zealand were co-enriched with other, butyrate-producing, taxa of the order Clostridiales. Conclusion: The TDA approach demonstrates the overlap and distinctions of microbiome composition between and within countries. This yields unique insights into complex associations in the dataset, a finding not possible with conventional approaches. It highlights the potential utility of TDA as a complementary tool in microbiome research, particularly for large population-scale datasets, and suggests further analysis on the effects of diet and other regionally varying factors.

Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective

As wheat (Triticum aestivum) is an important staple food across the world, preservation of stable yields and increased productivity are major objectives in breeding programs. Drought is a global concern because its adverse impact is expected to be amplified in the future due to the current climate change. Here, we analyzed the effects of edaphic, environmental, and host factors on the wheat root microbiomes collected in soils from six regions in Belgium. Amplicon sequencing analysis of unplanted soil and wheat root endosphere samples indicated that the microbial community variations can be significantly explained by soil pH, microbial biomass, wheat genotype, and soil sodium and iron levels. Under drought stress, the biodiversity in the soil decreased significantly, but increased in the root endosphere community, where specific soil parameters seemingly determine the enrichment of bacterial groups. Indeed, we identified a cluster of drought-enriched bacteria that significantly correlated with soil compositions. Interestingly, integration of a functional analysis further revealed a strong correlation between the same cluster of bacteria and β-glucosidase and osmoprotectant proteins, two functions known to be involved in coping with drought stress. By means of this in silico analysis, we identified amplicon sequence variants (ASVs) that could potentially protect the plant from drought stress and validated them in planta. Yet, ASVs based on 16S rRNA sequencing data did not completely distinguish individual isolates because of their intrinsic short sequences. Our findings support the efforts to maintain stable crop yields under drought conditions through implementation of root microbiome analyses.

Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics

Microbial communities are considered as vital members to reflect the health of a riverine system. Among them, pathogenic and fecal indicators imply health risks involved with potability of river water. The present study explores the diverse microbial communities, distribution pattern of potential pathogens, and fecal indicators between the geographically distinct Himalayan and Peninsular river systems of India. It also inquires into the environmental factors associated with community variance and distribution pattern of microbial indicators. The application of high-throughput amplicon sequencing approach unveiled significant demarcation (p < 0.004, Anosim R = 0.62) of samples suggesting unique microbial diversities in these two river sediments. Random forest analysis revealed Desulfobulbulus, PSB_M_3, and Opitutus in Himalayan, while DA101, Bacillus, and Streptomyces in the Peninsular as significant contributors to develop overall dissimilarity between the river systems. Permutational multivariate analysis of variance and co-occurrence network analysis were used to study the relationships between microbial taxa and environmental factors. Amongst the various studied environmental parameters, pH, K, Ca, Mg, Ba, and Al in the Himalayan and salinity, Na, temperature, and Th in the Peninsular significantly influenced shaping of distinct microbial communities. Furthermore, the potential pathogenic genera, including Flavobacterium, Clostridium, Arcobacter, Pseudomonas, and Bacillus were highly prevalent in both the river systems. Arcobacter, Clostridium, Acinetobacter, Bacteroides, and Caloramator were the prominent fecal indicators in these river systems. Our findings provide salient information about the crucial role and interplay between various environmental factors and anthropogenic influences in framing the microbiome of the distinct river systems in India. Moreover, assessing potential pathogenic and fecal indicators suggest the public health risk associated with untreated sewage discharge into these water sources. The detection of various F/S indicators and potentially pathogenic bacteria in Himalayan and Peninsular river systems emphasize the urgent need for future monitoring and management of major riverine systems in India.

Intercropping With Aromatic Plants Increased the Soil Organic Matter Content and Changed the Microbial Community in a Pear Orchard

Intercropping influences the soil microbiota via litter and root exudate inputs, but the mechanisms by which root exudates mediate the soil microbial community and soil organic matter (SOM) are still unclear. In this study, we selected three aromatic plants (Ocimum basilicum, Tr1; Satureja hortensis, Tr2; Ageratum houstonianum, Tr3) as intercrops that separately grew between rows of pear trees, and no plants were grown as the control in a pear orchard during the spring-summer season for 3 years. The soil from each plot was collected using a stainless-steel corer by five-point sampling between rows of pear trees. The bacterial and fungal communities of the different aromatic intercrops were analyzed by 16S and ITS rRNA gene amplicon sequencing; their functional profiles were predicted by PICRUSt and FUNGuild analyses. The root exudates of the aromatic plants were analyzed by a liquid chromatography-tandem mass spectrometry (LC-MS) system. Compared with the control treatment, all intercropping treatments with aromatic plants significantly increased SOM and soil water content and decreased pH values. The contents of total nitrogen and alkali-hydrolyzable nitrogen in Tr1 and Tr2 were higher than those in Tr3. In Tr3 soil, the relative content of saccharides increased little, whereas the changes in amine (increases) and alcohols (decreases) were rapid. Ageratum houstonianum intercropping decreased the microbial community diversity and significantly influenced the relative abundances of the dominant microbiota (Actinobacteria, Verrucomicrobia, Gemmatimonadetes, Cyanobacteria, Ascomycota, and Basidiomycota) at the phylum, class, and order levels, which increased the assemblage of functional groups (nitrite ammonification, nitrate ammonification, and ureolysis groups). Our study suggested that the main root exudates from aromatic plants shaped the microbial diversity, structure, and functional groups related to the N cycle during SOM mineralization and that intercropping with aromatic plants (especially basil and summer savory) increased N release in the orchard soil.

Role of environmental factors in shaping the soil microbiome

The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.

Impact of Temperature, Nutrients and Heavy Metals on Bacterial Diversity and Ecosystem Functioning Studied by Freshwater Microcosms and High-Throughput DNA Sequencing

Microbial communities are fundamental components in freshwater, and community shifts in ecosystem structure are indicative of changing environmental conditions. This study aimed at investigating the influence of key environmental parameters on bacterial diversity and ecosystem functioning (i.e. organic matter breakdown) in laboratory freshwater microcosms. The effects of varying temperatures (5, 20 and 35 °C), nutrients (representing low, medium and high urbanization) and heavy metals Copper (Cu) and Zinc (Zn) on bacterial diversity and organic matter (OM) breakdown were studied by using leaf bags and capsules filled with polycaprolactonediol-2000 (PCP-2000), respectively. The leaf-associated bacterial diversity was determined by next-generation sequencing of SSU rRNA gene amplicons. The results showed that bacterial diversity increased at high temperature (35 °C) with more operational taxonomic units (OTUs) as compared to medium (20 °C) or low (5 °C) temperatures, whereas nutrient variation had fewer effects on the bacterial community structure. In contrast, the presence of heavy metals, especially high concentrations (100 μM) of Cu, reduced the number of OTUs in the leaf-associated bacterial community. The higher temperatures and nutrient levels accelerated PCP-2000 breakdown rate, but this was impeded by a high concentration (100 μM) of Cu in the short term, though no effect of Zn on breakdown rate was observed. The overall results indicate that temperature and variated heavy metals are among the key factors that affect bacterial diversity and ecosystem functioning in freshwater systems.

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.

Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact

Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.

Changes in soil taxonomic and functional diversity resulting from gamma irradiation

Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of ⁶⁰Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAST. We hypothesized that with increasing radiation exposure there would be a decrease in both taxonomic and functional diversity. While bacterial diversity decreased, diversity of fungi and algae unexpectedly increased, perhaps because of release from competition. Despite the decrease in diversity of bacteria and of biota overall, functional gene diversity of algae, bacteria, fungi and total biota increased. Cycles of radiation exposure may increase the range of gene functional strategies viable in soil, a novel ecological example of the effects of stressors or disturbance events promoting some aspects of diversity. Moreover, repeated density-independent population crashes followed by population expansion may allow lottery effects, promoting coexistence. Radiation exposure produced large overall changes in community composition. Our study suggests several potential novel radiation-tolerant groups: in addition to Deinococcus-Thermus, which reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.

Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community

Heavy metal contamination is a serious problem worldwide threatening soil environment and human health. In the present study, concentrations of 6 heavy metals at an electronic waste (e-waste) site in Nigeria were correlated to their mobility, showing distinct distribution pattern between surface soils and subsoils. Proteobacteria, Firmicutes, Acidobacteria and Planctomycetes dominated the indigenous soil microbial communities, and there was significant discrimination of bacterial taxonomic composition between the heavy metal contaminated and uncontaminated areas. The abundance of most bacterial taxa changed with heavy metal contamination level to different extent. The multivariate regression tree (MRT) analyses illustrated that main environmental variables influencing bacterial taxonomic composition included soil texture (31%) and organic carbon (14%), whereas microbial diversity was affected by soil pH (32%) and soil texture (14%). Our results surprisingly indicated that soil properties were more influential in determining soil bacterial composition and diversity than heavy metals even at the e-waste site which was seriously contaminated by heavy metals. The present study contributes to a deeper insight into the key environmental variables shaping the diversity and composition of soil microbes at heavy metal contaminated e-waste sites.

Nutrient-uptake and -use efficiency in seedlings of rain-forest trees in New Caledonia: monodominants vs. subordinates and episodic vs. continuous regenerators

The upper canopy of some rain forests in New Caledonia is dominated by single species. These monodominants are commonly secondary species, their dominance not persisting without disturbance. We tested whether dominance is associated with efficient uptake and use of nutrients (N, P and K), comparing between seedlings of monodominants (Nothofagus spp., Arillastrum gummiferum and Cerberiopsis candelabra) and 14 subordinates, grown in a nursery house. We also tested whether this trend applies more broadly to shade-intolerant trees that regenerate episodically (ER species) versus shade-tolerant trees that regenerate continuously (CR species). In the sun treatment, monodominants had higher photosynthetic nutrient-use efficiency and productivity for N and K, and uptake efficiency for N, P and K, than subordinates; ER species had higher photosynthetic nutrient-use efficiency for N, P and K, and uptake efficiency for N and P, than CR species. Uptake efficiency and productivity per nutrient mass were uncorrelated across species, yet Nothofagus spp., A. gummiferum and C. candelabra combined high levels of both traits for N, and Nothofagus spp. and A. gummiferum combined moderate to high levels for P, in sun-grown seedlings. This trait combination may contribute substantially to competitiveness and post-disturbance dominance on these nutrient-poor soils.