Soil-borne microbiome: linking diversity to function

Redox conditions and biochar pyrolysis temperature affecting As and Pb biogeochemical cycles and bacterial community of sediment from mining tailings

Despite the widespread use of biochar for soil and sediment remediation, little is known about the impact of pyrolysis temperature on the biogeochemistry of arsenic (As) and lead (Pb) and microorganisms in sediment under reducing conditions. In this study, we investigated the effects of pyrolysis temperature and the addition of glucose on the release and transformation of As and Pb, as well as their potential effects on the bacterial community in contaminated sediments. The addition of biochar altered the geochemical cycle of As, as it favors specific bacterial groups capable of changing species from As(V) to As(III) through fermentation, sulfate respiration and nitrate reduction. The carbon quality and content of N and S in solution shaped the pH and redox potential in a way that changed the microbial community, favoring Firmicutes and reducing Proteobacteria. This change played a fundamental role in the reductive dissolution of As and Pb minerals. The addition of biochar was the only efficient way to remove Pb, possibly as a function of its sorption and precipitation mechanisms. Such insights could contribute to the production or choice of high-efficiency biochar for the remediation of sediments subjected to redox conditions.

Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens

The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.

Functional guilds and drivers of diversity in seaweed-associated bacteria

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution

Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.

Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential

BACKGROUND

Bacterial communities are critical to ecosystem functioning and sensitive to their surrounding physiochemical environment. However, the impact of land use change on microbial communities remains understudied. We used 16S rRNA gene amplicon sequencing and shotgun metagenomics to assess soil microbial communities' taxonomic and functional responses to land use change. We compared data from long-term grassland, exotic forest and horticulture reference sites to data from sites that transitioned from (i) Grassland to exotic forest or horticulture and from (ii) Exotic forest to grassland.

RESULTS

Community taxonomic and functional profiles of the transitional sites significantly differed from those within reference sites representing both their historic and current land uses (P < 0.001). The bacterial communities in sites that transitioned more recently were compositionally more similar to those representing their historic land uses. In contrast, the composition of communities from sites exposed to older conversion events had shifted towards the compositions at reference sites representing their current land use.

CONCLUSIONS

Our study indicates that microbial communities respond in a somewhat predictable way after a land use conversion event by shifting from communities reflecting their former land use towards those reflecting their current land use. Our findings help us to better understand the legacy effects of land use change on soil microbial communities and implications for their role in soil health and ecosystem functioning. Understanding the responsiveness of microbial communities to environmental disturbances will aid us in incorporating biotic variables into soil health monitoring techniques in the future.

Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert

Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity. However, little is known about the identities and communities of phyllosphere epiphytic microorganisms inhabiting the xerophyte leaf surface in the hot and dry environment. The diversity and community composition of phyllosphere epiphytes on different desert plants in Gansu, China, was investigated using the next-generation sequencing technique, revealing the diversity and community composition of the phyllosphere epiphytic bacteria associated with desert xerophytes. In addition, the ecological functions of the bacterial communities were investigated by combining the sequence classification information and prokaryotic taxonomic function annotation (FAPROTAX). This study determined the phyllosphere bacterial community composition, microbial interactions, and their functions. Despite harsh environments in the arid desert, we found that there are still diverse epiphytic bacteria on the leaves of desert plants. The bacterial communities mainly included Actinobacteria (52.79%), Firmicutes (31.62%), and Proteobacteria (12.20%). Further comparisons revealed different microbial communities, including Firmicutes at the phylum and Paenibacillaceae at the family level, in the phyllosphere among different plants, suggesting that the host plants had strong filter effects on bacteria. Co-occurrence network analysis revealed positive relationships were dominant among different bacterial taxa. The abundance of Actinobacteria and Proteobacteria was positively correlated, demonstrating their mutual relationship. On the other hand, the abundance of Firmicutes was negatively correlated, which suggested that they inhibit the growth of other bacterial taxa. FAPROTAX prediction revealed that chemoheterotrophy (accounting for 39.02% of the community) and aerobic chemoheterotrophy (37.01%) were the main functions of the leaf epiphytic bacteria on desert plants. This study improves our understanding of the community composition and ecological functions of plant-associated microbial communities inhabiting scattered niches in the desert ecosystem. In addition, the study provides insight into the biodiversity assessment in the desert region.

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.

Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards

Soil tillage or herbicide applications are commonly used in agriculture for weed control. These measures may also represent a disturbance for soil microbial communities and their functions. However, the generality of response patterns of microbial communities and functions to disturbance have rarely been studied at large geographical scales. We investigated how a soil disturbance gradient (low, intermediate, high), realized by either tillage or herbicide application, affects diversity and composition of soil bacterial and fungal communities as well as soil functions in vineyards across five European countries. Microbial alpha-diversity metrics responded to soil disturbance sporadically, but inconsistently across countries. Increasing soil disturbance changed soil microbial community composition at the European level. However, the effects of soil disturbance on the variation of microbial communities were smaller compared to the effects of location and soil covariates. Microbial respiration was consistently impaired by soil disturbance, while effects on decomposition of organic substrates were inconsistent and showed positive and negative responses depending on the respective country. Therefore, we conclude that it is difficult to extrapolate results from one locality to others because microbial communities and environmental conditions vary strongly over larger geographical scales.

Evaluation of nitrogen removal, functional gene abundance and microbial community structure in a stormwater detention basin

Stormwater control measures such as detention basins are used to mitigate the negative effects of urban stormwater resulting from watershed development. In this study, the performance of a detention basin in mitigating nitrogen pollution was examined and the abundance of N-cycling genes (amoA, nirK, nosZ, hzsB and Ntsp-amoA) present in the soil media of the basin was measured using quantitative PCR. Results showed a net export of nitrogen from the basin, however, differences between in- and outflow concentrations were not significant. Furthermore, the quantitative PCR showed that nirK (denitrification gene) was more abundant in the winter season, whereas amoA (nitrification gene) was more abundant in the summer season. The abundance of nirK, Ntsp-amoA and hzsB genes also varied with the sampling depth of soil and based on 16S rRNA gene sequencing of soil samples, Actinobacteria and Proteobacteria were the most dominant phyla. Species diversity appeared higher in summer, while the top and bottom layer of soil clustered separately based on the bacterial community structure. These results underline the importance of understanding nitrogen dynamics and microbial processes within stormwater control measures to enhance their design and performance.

Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential

The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.

Bacterial functional redundancy and carbon metabolism potentials in soil, sediment, and water of thermokarst landscapes across the Qinghai-Tibet Plateau: Implications for the fate of permafrost carbon

Permafrost thaw create widespread thermokarst landscapes. As a result, distinct habitats are provided to harbor different bacterial communities in degraded permafrost soil (PBCs), thermokarst lake sediment (SBCs), and lake water (WBCs), driving carbon metabolism differentially. In this study, we investigated functional diversity and redundancy, and carbon metabolism potentials of PBCs, SBCs, and WBCs in thermokarst landscapes across the Qinghai-Tibet Plateau. The results showed that PBCs and SBCs had higher taxonomic and functional alpha diversity than WBCs, while WBCs had lower functional redundancy. WBCs had the highest beta diversity followed by SBCs and PBCs, suggesting strong determination of taxonomic variations on functional differences. Community assembly processes also had significant influences on beta diversity, especially for SBCs. Metabolism pathways of carbohydrate metabolism, methane metabolism, and carbon fixation were enriched differentially in PBCs, SBCs, and WBCs, suggesting different C fate in distinct habitats. Carbohydrate metabolism data suggested that PBCs might have stronger potentials to mineralize a greater diversity of organic carbon substrate than SBCs and WBCs, promoting degradation of organic carbon stocks in degraded permafrost soils. Methane metabolism data showed that SBCs had a stronger methanogenesis potential followed by PBCs and WBCs, while PBCs had a stronger methane oxidation potential. High abundance of genes involving in formaldehyde assimilation might suggested that a large proportion of produced methane might be assimilated by methanotrophs in the thermokarst landscapes. Both aerobic and anaerobic carbon fixation pathways were enriched in PBCs. The results added our understanding of functional properties and biogeochemical carbon cycles in thermokarst landscapes, improving our abilities in accurate modeling of carbon dynamics and the ultimate fate of permafrost carbon in a warming world.

Metabolic fates and response strategies of microorganisms to aromatic compounds with different structures

In this study, the metabolic fates and response strategies of microorganisms to aromatic compounds with different structures (phenol, naphthalene, phenanthrene, and pyrene) were comparatively studied. The results indicated that the phenol (90.9%), naphthalene (68.4%), phenanthrene (69.5%), and pyrene (67.1%) could be mineralized, and the biotoxicity also has been drastically reduced. The degradation characteristics and toxic effects were closely related to their chemical structure. The microorganisms showed different response strategies to aromatic compounds with different structures. Phenol had a simple structure and low toxicity, the microbial community structure was simple, and the rapid expression of key enzymes enabled it to be rapidly degraded. For the hydrophobic and complex naphthalene, phenanthrene, and pyrene, the more complex the structure, the higher the microbial diversity, the EPS showed different response for the purpose of improving their bioavailability, and the activity of key enzymes was positively correlated with their structural complexity.

Bacterial Community Structure and Function Shift in Rhizosphere Soil of Tobacco Plants Infected by Meloidogyne incognita

Root-knot nematode disease is a widespread and catastrophic disease of tobacco. However, little is known about the relationship between rhizosphere bacterial community and root-knot nematode disease. This study used 16S rRNA gene sequencing and PICRUSt to assess bacterial community structure and function changes in rhizosphere soil from Meloidogyne incognita-infected tobacco plants. We studied the rhizosphere bacterial community structure of M. incognita-infected and uninfected tobacco plants through a paired comparison design in two regions of tobacco planting area, Yuxi and Jiuxiang of Yunnan Province, southwest China. According to the findings, M. incognita infection can alter the bacterial population in the soil. Uninfested soil has more operational taxonomic unit numbers and richness than infested soil. Principal Coordinate Analysis revealed clear separations between bacterial communities from infested and uninfested soil, indicating that different infection conditions resulted in significantly different bacterial community structures in soils. Firmicutes was prevalent in infested soil, but Chloroflexi and Acidobacteria were prevalent in uninfested soil. Sphingomonas, Streptomyces, and Bradyrhizobium were the dominant bacteria genera, and their abundance were higher in infested soil. By PICRUSt analysis, some metabolism-related functions and signal transduction functions of the rhizosphere bacterial community in the M. incognita infection-tobacco plants had a higher relative abundance than those uninfected. As a result, rhizosphere soils from tobacco plants infected with M. incognita showed considerable bacterial community structure and function alterations.

Effect of marigold (Tagetes erecta L.) on soil microbial communities in continuously cropped tobacco fields

Root-knot nematode disease is a catastrophic soil-borne disease in tobacco production. The regulation of natural microbial communities is considered a good disease management approach to suppress the incidence of soilborne diseases. In this study, the effects of tobacco (Nicotiana tabacum L.)-marigold (Tagetes erecta L.) rotation on the diversity and structure of soil microbial communities in continuously cropped tobacco fields were analyzed to manage this devastating pathogen. The results showed that the soil bacterial OTUs increased after marigold rotation and that the bacterial Shannon, ACE, Chao1 index, and fungal Shannon index were higher in the tobacco-marigold rotation fields than in the continuously cropped tobacco fields by 3.98%, 10.37%, 5.46%, and 3.43%, respectively. After marigold rotation, the relative abundances of Actinobacteria, Acidobacteria, and Ascomycota increased by 28.62%, 107.50%, and 57.44%, respectively, and the proportion of beneficial bacterial genera such as Nocardioides, Gemmatimonas, and Bradyrhizobium increased. In addition, our results also showed that rotation of marigold could effectively reduce the incidence of root-knot nematodes in the next crop of tobacco. These results indicate that marigold rotation had a positive effect on the soil microecological environment of continuously cropped tobacco fields, reducing the obstacles to continuous cropping of tobacco.

Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.

Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges

Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.

Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities

Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.

One or many? Multi-species livestock grazing influences soil microbiome community structure and antibiotic resistance potential

Soil health has been highlighted as a key dimension of regenerative agriculture, given its critical importance for food production, carbon sequestration, water filtration, and nutrient cycling. Microorganisms are critical components of soil health, as they are responsible for mediating 90% of soil functions. Multi-species rotational grazing (MSRG) is a promising strategy for maintaining and improving soil health, yet the potential effects of MSRG on soil microbiomes are poorly understood. To address this knowledge gap, we collected soil microbial samples at three timepoints during the 2020 grazing season for 12 total paddocks, which were equally split into four different grazing treatments—cattle only, sheep only, swine only, or multi-species. Shallow shotgun metagenomic sequencing was used to characterize soil microbial community taxonomy and antibiotic resistome. Results demonstrated broad microbial diversity in all paddock soil microbiomes. Samples collected early in the season tended to have greater archaeal and bacterial alpha diversity than samples collected later for all grazing treatments, while no effect was observed for fungi or viruses. Beta diversity, however, was strongly influenced by both grazing treatment and month for all microbial kingdoms, suggesting a pronounced effect of different livestock on microbial composition. Cattle-only and swine-only paddocks were more dissimilar from multi-species paddocks than those grazed by sheep. We identified a large number of differentially abundant taxa driving community dissimilarities, including Methanosarcina spp., Candidatus Nitrocosmicus oleophilus, Streptomyces spp., Pyricularia spp., Fusarium spp., and Tunggulvirus Pseudomonas virus ϕ-2. In addition, a wide variety of antibiotic resistance genes (ARGs) were present in all samples, regardless of grazing treatment; the majority of these encoded efflux pumps and antibiotic modification enzymes (e.g., transferases). This novel study demonstrates that grazing different species of livestock, either separately or together, can impact soil microbial community structure and antibiotic resistance capacity, though further research is needed to fully characterize these impacts. Increasing the knowledge base about soil microbial community structure and function under real-world grazing conditions will help to construct metrics that can be incorporated into traditional soil health tests and allow producers to manage livestock operations for optimal soil microbiomes.

Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.

Effect of Bacterial Wilt on Fungal Community Composition in Rhizosphere Soil of Tobaccos in Tropical Yunnan

Bacterial wilt, which is a major soil-borne disease with widespread occurrence, poses a severe danger in the field of tobacco production. However, there is very limited knowledge on bacterial wilt-induced microecological changes in the tobacco root system and on the interaction between Ralstonia solanacearum and fungal communities in the rhizosphere soil. Thus, in this study, changes in fungal communities in the rhizosphere soil of tobaccos with bacterial wilt were studied by 18S rRNA gene sequencing. The community composition of fungi in bacterial wilt-infected soil and healthy soil in two tobacco areas (Gengma and Boshang, Lincang City, Yunnan Province, China) was studied through the paired comparison method in July 2019. The results showed that there were significant differences in fungal community composition between the rhizosphere soil of diseased plants and healthy plants. The changes in the composition and diversity of fungal communities in the rhizosphere soil of tobaccos are vital characteristics of tobaccos with bacterial wilt, and the imbalance in the rhizosphere microecosystem of tobacco plants may further aggravate the disease.

Responses of Soil Microbiota to Different Control Methods of the Spartina alterniflora in the Yellow River Delta

Spartina alterniflora invasion has negative effects on the structure and functioning of coastal wetland ecosystems. Therefore, many methods for controlling S. alterniflora invasion have been developed. S. alterniflora control methods can affect plant community, which results in changes in microbial communities and subsequent changes in soil ecological processes. However, the effects of controlling S. alterniflora on soil microbial communities remain poorly understood. We aimed to examine the responses of bacterial and fungal communities to invasion control methods (cutting plus tilling treatment: CT; mechanical rolling treatment: MR). Soil bacterial and fungal community diversity and composition structure were assessed using high-throughput sequencing technology. The findings of the study showed that bacterial diversity and richness in the CT treatment reduced substantially, but fungal diversity and richness did not show any remarkable change. Bacterial and fungal diversity and richness in the MR treatment were not affected considerably. In addition, the two control methods significantly changed the soil microbial community structure. The relative abundance of bacteria negatively associated with nutrient cycling increased considerably in the CT treatment. The considerable increases in the relative abundance of certain bacterial taxa in the MR treatment may promote soil nutrient cycling. Compared with mechanical rolling, soil bacterial community diversity and structure were more sensitive to cutting plus tilling.

Plant diversity and soil properties regulate the microbial community of monsoon evergreen broad-leaved forest under different intensities of woodland use

A key aspect of global forest management, woodland use intensity (WUI) greatly affects the composition and diversity of soil microbial communities, thereby affecting multiple ecosystem functions and services. However, the effects of WUI on soil microbial community composition and enzymatic activities remains unclear. The effects of anthropomorphic alterations to a natural monsoon evergreen broad-leaved forest in terms of the composition and diversity of soil fungal and bacterial communities, was investigated at a site in Yunnan Province, Southwest China. Soil microbial communities were assessed under four levels of disturbance with increasing levels of WUI: (i) none, undisturbed forest (control), (ii) light, naturally-regenerated Pinus kesiya Royle ex Gordon forest, (iii) intermediate, shrub and grassland communities formed through grazing, and (iv) severe, continuously managed coffee (Coffea arabica L.) plantations. With increasing WUI, the diversity of soil fungal and bacterial communities increased, while similarities in community composition decreased for fungi but increased for bacteria. Among fungal functional guilds, ectomycorrhizal fungi decreased significantly with increasing WUI, whereas saprotrophic fungi (undefined, wood, and soil saprotrophs) increased significantly. The species richness of woody plants remarkably affected fungal functional guilds. Ectomycorrhizal fungi interacted in a synergistic manner with the fungal network structure. Significantly affecting microorganismal network structure, WUI increases led to more homogeneous networks with less integration within modules within the microbial community. The WUI strongly altered hub identity and module composition in the microbial community. According to structural equation models, WUI had direct positive effects on soil fungal community composition via its effects on plant species richness. The diversity of bacterial and fungal communities and composition of bacterial communities were jointly regulated by the indirect effects of plant species richness and soil nutrients (including enzyme activity). Deterministic processes largely determined the composition of soil fungal and bacterial communities. This study highlights the importance of maintaining the diversity of soil fungal and bacterial communities despite changes in woodland use to sustain ecosystem functions. These results can be used to develop management practices in subtropical forests and help sustain plant and soil microbial diversity at levels sufficient to maintain long-term ecosystem function and services.

Characterization of Rhizosphere Microbial Communities for Disease Incidence and Optimized Concentration of Difenoconazole Fungicide for Controlling of Wheat Dwarf Bunt

Rhizosphere soil microorganisms have great agricultural importance. To explore the relationship between rhizosphere microorganisms and the disease incidence, and to optimize the concentration of difenoconazole fungicide for the control of wheat dwarf bunt, caused by Tilletia controversa Kühn, the rhizosphere microorganisms were characterized based on sequencing methods. We found that the disease incidence correlated with the relative abundance of some microbial communities, such as Acidobacteria, Nocardioides, Roseiflexaceae, Pyrinomonadaceae, and Gemmatimonadaceae. Actinobacteria showed significant differences in the infected soils when compared to the control soils, and the relative abundance of Acidobacteria, Pyrinomonadaceae, Gemmatimonadaceae, and Saccharimonadales populations was distinctly higher in the T. controversa-inoculated group than in the control group. The members of Dehalococcoidia, Nitrosomonadaceae, and Thermomicrobiales were found only in T. controversa-inoculated soils, and these taxa may have potential effects against the pathogen and contribute to disease control of wheat dwarf bunt. In addition, for T. controversa-infected plants, the soil treated with difenoconazole showed a high relative abundance of Proteobacteria, Actinobacteria, Ascomycota, Basidiomycota, Mortierellomycota, and Olpidiomycota based on the heatmap analysis and ANOVA. Our findings suggest that the optimized concentration of fungicide (5% recommended difenoconazole) exhibits better control efficiency and constant diversity in the rhizosphere soil.

Metagenomics: A New Direction in Ecology

Abstract

The prospects for application of metagenomic technologies in environmental studies are discussed. The advantages in investigating the taxonomic composition of aquatic and terrestrial ecosystems, as well as examples of trophic and phoric relationships found in ecosystems using the metagenomic approach, are described. The capabilities of metagenomics to study prokaryotic communities in complicated environments such as soils or animal intestines are shown. The role of relic DNA in the metagenome and the possibilities to study ancient organisms are highlighted. Particular attention is paid to the criticism of metagenomic technologies related to the low reproducibility of the sequencing data. Common methodological mistakes in bioinformatics processing of metagenomic data leading to misleading results are considered.

Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga

Soils comprise a huge fraction of the world's biodiversity, contributing to several crucial ecosystem functions. However, how the forest-to-pasture conversion impact soil bacterial diversity remains poorly understood, mainly in the Caatinga biome, the largest tropical dry forest of the world. Here, we hypothesized that forest-to-pasture conversion would shape the microbial community. Thus, the soil bacterial community was assessed using the 16S rRNA gene sequencing into the Illumina MiSeq platform. Then, we analyzed ecological patterns and correlated the bacterial community with environmental parameters in forest, and two distinct pastures areas, one less productive and another more productive. The variation in soil properties in pastures and forest influenced the structure and diversity of the bacterial community. Thus, the more productive pasture positively influenced the proportion of specialists and the co-occurrence network compared to the less productive pasture. Also, Proteobacteria, Acidobacteria, and Verrucomicrobia were abundant under forest, while Actinobacteria, Firmicutes, and Chloroflexi were abundant under pastures. Also, the more productive pasture presented a higher bacterial diversity, which is important since that a more stable and connected bacterial community could benefit the agricultural environment and enhance plant performance, as can be observed by the highest network complexity in this pasture. Together, our findings elucidate a significant shift in soil bacterial communities as a consequence of forest-to-pasture conversion and bring important information for the development of preservation strategies.

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

Soil Nitrogen Treatment Alters Microbiome Networks Across Farm Niches

Agriculture is fundamental for food production, and microbiomes support agriculture through multiple essential ecosystem services. Despite the importance of individual (i.e., niche specific) agricultural microbiomes, microbiome interactions across niches are not well-understood. To observe the linkages between nearby agricultural microbiomes, multiple approaches (16S, 18S, and ITS) were used to inspect a broad coverage of niche microbiomes. Here we examined agricultural microbiome responses to 3 different nitrogen treatments (0, 150, and 300 kg/ha/yr) in soil and tracked linked responses in other neighbouring farm niches (rumen, faecal, white clover leaf, white clover root, rye grass leaf, and rye grass root). Nitrogen treatment had little impact on microbiome structure or composition across niches, but drastically reduced the microbiome network connectivity in soil. Networks of 16S microbiomes were the most sensitive to nitrogen treatment across amplicons, where ITS microbiome networks were the least responsive. Nitrogen enrichment in soil altered soil and the neighbouring microbiome networks, supporting our hypotheses that nitrogen treatment in soil altered microbiomes in soil and in nearby niches. This suggested that agricultural microbiomes across farm niches are ecologically interactive. Therefore, knock-on effects on neighbouring niches should be considered when management is applied to a single agricultural niche.

Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis

Exploring microbial community compositions in humans with healthy versus diseased states is crucial to understand the microbe-host interplay associated with the disease progression. Although the relationship between oral cancer and microbiome was previously established, it remained controversial, and yet the ecological characteristics and their responses to oral carcinogenesis have not been well studied. Here, using the bacterial 16S rRNA gene amplicon sequencing along with the in silico function analysis by PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2), we systematically characterized the compositions and the ecological drivers of saliva microbiome in the cohorts of orally healthy, non-recurrent oral verrucous hyperplasia (a pre-cancer lesion), and oral verrucous hyperplasia–associated oral cancer at taxonomic and function levels, and compared them with the re-analysis of publicly available datasets. Diversity analyses showed that microbiome dysbiosis in saliva was significantly linked to oral health status. As oral health deteriorated, the number of core species declined, and metabolic pathways predicted by PICRUSt2 were dysregulated. Partitioned beta-diversity revealed an extremely high species turnover but low function turnover. Functional beta-diversity in saliva microbiome shifted from turnover to nestedness during oral carcinogenesis, which was not observed at taxonomic levels. Correspondingly, the quantitative analysis of stochasticity ratios showed that drivers of microbial composition and functional gene content of saliva microbiomes were primarily governed by the stochastic processes, yet the driver of functional gene content shifted toward deterministic processes as oral cancer developed. Re-analysis of publicly accessible datasets supported not only the distinctive family taxa of Veillonellaceae and Actinomycetaceae present in normal cohorts but also that Flavobacteriaceae and Peptostreptococcaceae as well as the dysregulated metabolic pathways of nucleotides, amino acids, fatty acids, and cell structure were related to oral cancer. Using predicted functional profiles to elucidate the correlations to the oral health status shows superior performance than using taxonomic data among different studies. These findings advance our understanding of the oral ecosystem in relation to oral carcinogenesis and provide a new direction to the development of microbiome-based tools to study the interplay of the oral microbiome, metabolites, and host health.

Legacy effects of temporary grassland in annual crop rotation on soil ecosystem services

The introduction of temporary grassland into an annual crop rotation is recognized to improve soil ecosystem services, and resulting legacies can be beneficial for the following crops. In this context, the aim of the present study was to evaluate legacy effects of introducing temporary grassland into an annual crop rotation on five ecosystem services (i) soil structure maintenance (aggregate stability), (ii) water regulation (saturated hydraulic conductivity), (iii) biodiversity conservation (microbial biomass and microbial metabolic activity, as well as microorganism, enchytraeid, springtail and earthworm communities), (iv) pathogen regulation (soil suppressiveness to Verticillium dahliae), and (v) forage production and quality. Three crop rotation schemes, maintained for twelve years, were compared in four random blocks, one being an annual crop rotation without grassland (0%), another with a medium percentage of grassland (50%, corresponding to 3 years of continuous grassland in the crop rotation), and a third one with a high percentage of grassland in the crop rotation (75%, corresponding to 6 years of continuous grassland in the crop rotation). The results showed that the grassland introduction into an annual crop rotation improved, whatever the duration of the grassland, soil structure maintenance and biodiversity conservation, while it decreased pathogen regulation and did not modify water regulation. Comparing the two crop rotations that included grassland, indicated a stronger beneficial grassland legacy effect for the higher proportion of grassland concerning soil structure maintenance and biodiversity conservation. By contrast, water regulation, pathogen regulation and forage production were not affected by the legacy of the 75% grassland during the rotation. Overall, our findings demonstrated the extent to which grassland legacies are affecting the current state of soil properties and possible ecosystem services provided. To improve ecosystem services, soil management should take legacy effects into account and consider longer timeframes to apply beneficial practices.

Microbiota modulation of allelopathy depends on litter chemistry: Mitigation or exacerbation?

Having a pivotal role in biogeochemical cycles, litter decomposition affects plant growth and regeneration by inducing the release of allelochemicals. The aim of this study was to assess the role of the microbiota in modulating the allelopathic effects of freshly fallen and decomposed leaf litter. To disentangle the chemical and microbial effects, bioassays were carried out on four target plants in sterile and non-sterile conditions. All litter types were characterized by carbon-13 cross polarization magic-angle spinning nuclear magnetic resonance (¹³C-CPMAS NMR) spectroscopy, and the associated fungal and bacterial microbiota were described by next-generation sequencing. When the litter extract was sterilized, freshly fallen litter severely inhibited the plant root growth, but during decomposition, the allelopathic effect rapidly decreased. Root growth was negatively correlated with extractable carbon and positively correlated with parameters associated with tissue lignification. In non-sterile conditions, the living microbiota modulated the leaf litter allelopathic effects of mitigation (26.5% of cases) and exacerbation (26.6% of cases). The mitigation effect was more frequent and intense in stressful conditions, i.e., highly phytotoxic freshly fallen litter, than in benign environments, i.e., decomposed litter. Finally, we identified specific bacterial and fungal operational taxonomic units (OTUs) that could be involved in the mediation of the litter allelopathic effect. This study highlights the importance of studying allelopathy in both sterile conditions and in the presence of a living microbiota to assess the role of litter chemistry and the potential impact of plant detritus on the agro-ecosystem and natural plant communities.

Composted biochar affects structural dynamics, function and co-occurrence network patterns of fungi community

A few researchers have reported enhancing soil physicochemical properties and reducing greenhouse gas emission using biochar-compost mixture as an alternative method to address soil fertility, soil degradation and climate change. However, information about its effects on soil microbiome has rarely been studied. This investigation was on the impact of a combined biochar-compost application on soil physicochemical variables, fungal community composition, function and network patterns in maize at seedling stage (SS), reproductive stage (RS), and maturity stage (MS). The experimental design consists of five treatments: control (CNT), compost (CMP), composted biochar (CMB), compost fortified with biochar (CFWB), biochar (BCH). The results showed that CFWB, CMB, and CMP increased fungal diversity indices (Shannon, Sobs, and Chao) at the RS and MS stages respectively, compared to BCH and CNT. Distance-based redundancy analysis (db-RDA) at genus level indicated that the pH, available nitrogen, and soil organic matter at SS; available phosphorus at RS; Mg, Mn, Fe, and Zn at MS significantly and positively affected the fungi community. Based on the Linear discriminant analysis (LDA) and effect size (LEfSe) analysis, the results revealed that only Cystofilobasidiaceae and Guehomyces were the MS biomarkers; and significantly enriched in CFWB. FUNGuild analysis indicated that organic amendments (CFWB, CMB, CMP, and BCH) suppressed the abundance of plant pathogenic fungi (Edenia and Waitea) compared to CNT. Network analysis showed that CFWB and CMB had a high niche overlap and cross-feeding in their networks compared to other treatments. However, CMP network had more positive links with Saprotroph, Pathotroph-Saprotroph-Symbiotroph, Pathotroph and Pathotroph-Symbiotroph compared with other treatments. This study showed that applying biochar, compost and a mixture of both, positively affected soil fungal communities plus co-occurrence network pattern in a single cropping season. Thus, their application as soil amendments may improve the soil fungi ecosystem, soil health and quality and mitigate climate change.

Lutzomyia longipalpis Antimicrobial Peptides: Differential Expression during Development and Potential Involvement in Vector Interaction with Microbiota and Leishmania

Antimicrobial peptides (AMPs) are produced to control bacteria, fungi, protozoa, and other infectious agents. Sand fly larvae develop and feed on a microbe-rich substrate, and the hematophagous females are exposed to additional pathogens. We focused on understanding the role of the AMPs attacin (Att), cecropin (Cec), and four defensins (Def1, Def2, Def3, and Def4) in Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas. Larvae and adults were collected under different feeding regimens, in addition to females artificially infected by Leishmania infantum. AMPs’ gene expression was assessed by qPCR, and gene function of Att and Def2 was investigated by gene silencing. The gene knockdown effect on bacteria and parasite abundance was evaluated by qPCR, and parasite development was verified by light microscopy. We demonstrate that L. longipalpis larvae and adults trigger AMPs expression during feeding, which corresponds to an abundant presence of bacteria. Att and Def2 expression were significantly increased in Leishmania-infected females, while Att suppression favored bacteria growth. In conclusion, L. longipalpis AMPs’ expression is tuned in response to bacteria and parasites but does not seem to interfere with the Leishmania cycle.

The profile of the soil microbiota in the Cerrado is influenced by land use

Extensive areas of the Cerrado biome have been deforested by the rapid advance of agricultural frontiers, especially by agricultural monocultures, and cultivated pastures. The objective of this study was to characterize the soil microbial community of an environment without anthropogenic interference and to compare it with soybean soil and pasture areas. For that, metagenomic sequencing techniques of the 16S rRNA gene were employed. Consistent changes in the profiles of diversity and abundance were described between communities in relation to the type of soil. The soil microbiome of the native environment was influenced by the pH level and content of Al³⁺, whereas the soil microbiomes cultivated with soybean and pasture were associated with the levels of nutrients N and P and the ions Ca²⁺ and Mg²⁺, respectively. The analysis of bacterial communities in the soil of the native environment showed a high abundance of members of the Proteobacteria phylum, with emphasis on the Bradyrhizobium and Burkholderia genera. In addition, significant levels of species of the Bacillus genus, and Dyella ginsengisoli, and Edaphobacter aggregans of the Acidobacteria phylum were detected. In the soil community with soybean cultivation, there was a predominance of Proteobacteria, mainly of the Sphingobium and Sphingomonas genera. In the pasture, the soil microbiota was dominated by the Firmicutes, which was almost entirely represented by the Bacillus genus. These results suggest an adaptation of the bacterial community to the soybean and pasture cultivations and will support understanding how environmental and anthropogenic factors shape the soil microbial community. KEY POINTS: • The Cerrado soil microbiota is sensitive to impacts on the biome. • Microbial communities have been altered at all taxonomic levels.

Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community

Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer soil microbial community composition by applying organic amendments to the soil.

Enhancing soil suppressiveness against plant pathogens or pests is a promising alternative strategy to chemical pesticides. Organic amendments have been shown to reduce crop diseases and pests, with chitin products the most efficient against fungal pathogens. To study which characteristics of organic products are correlated with disease suppression, an experiment was designed in which 10 types of organic amendments with different physicochemical properties were tested against the soilborne pathogen Rhizoctonia solani in sugar beet seedlings. Organic amendments rich in keratin or chitin reduced Rhizoctonia solani disease symptoms in sugar beet plants. The bacterial and fungal microbial communities in amended soils were distinct from the microbial communities in nonamended soil, as well as those in soils that received other nonsuppressive treatments. The Rhizoctonia-suppressive amended soils were rich in saprophytic bacteria and fungi that are known for their keratinolytic and chitinolytic properties (i.e., Oxalobacteraceae and Mortierellaceae). The microbial community in keratin- and chitin-amended soils was associated with higher zinc, copper, and selenium, respectively.

IMPORTANCE Our results highlight the importance of soil microorganisms in plant disease suppression and the possibility to steer soil microbial community composition by applying organic amendments to the soil.

Urbanization pressures alter tree rhizosphere microbiomes

The soil microbial community (SMC) provides critical ecosystem services including organic matter decomposition, soil structural formation, and nutrient cycling. Studies suggest plants, specifically trees, act as soil keystone species controlling SMC structure via multiple mechanisms (e.g., litter chemistry, root exudates, and canopy alteration of precipitation). Tree influence on SMC is shaped by local/regional climate effects on forested environments and the connection of forests to surrounding landscapes (e.g., urbanization). Urban soils offer an ideal analog to assess the influence of environmental conditions versus plant species-specific controls on SMC. We used next generation high throughput sequencing to characterize the SMC of specific tree species (Fagus grandifolia [beech] vs Liriodendron tulipifera [yellow poplar]) across an urban-rural gradient. Results indicate SMC dissimilarity within rural forests suggests the SMC is unique to individual tree species. However, greater urbanization pressure increased SMC similarity between tree species. Relative abundance, species richness, and evenness suggest that increases in similarity within urban forests is not the result of biodiversity loss, but rather due to greater overlap of shared taxa. Evaluation of soil chemistry across the rural-urban gradient indicate pH, Ca⁺, and organic matter are largely responsible for driving relative abundance of specific SMC members.

Microbiological Study in Petrol-Spiked Soil

The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition-with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon-Weaver's index of bacterial taxa diversity (H); and Shannon-Weaver's index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. The least susceptible to the soil pollution with petrol and cocksfoot cultivation were the bacteria of the following genera: Kaistobacter, Rhodoplanes, Bacillus, Streptomyces, Paenibacillus, Phenylobacterium, and Terracoccus. Cocksfoot proved effective in the phytoremediation of petrol-polluted soil, as it accelerated hydrocarbon degradation and increased the genetic diversity of bacteria. It additionally enhanced the activities of soil enzymes.

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas

Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.

Composition of soil bacterial and fungal communities in relation to vegetation composition and soil characteristics along an altitudinal gradient

The objective of the present study was to evaluate how altitudinal gradients shape the composition of soil bacterial and fungal communities, humus forms and soil properties across six altitude levels in Hyrcanian forests. Soil microbiomes were characterized by sequencing amplicons of selected molecular markers. Soil chemistry and plant mycorrhizal type were the two dominant factors explaining variations in bacterial and fungal diversity, respectively. The lowest altitude level had more favorable conditions for the formation of mull humus and exhibited higher N and Ca contents. These conditions were also associated with a higher proportion of Betaproteobacteria, Acidimicrobia, Acidobacteria and Nitrospirae. Low soil and forest floor quality as well as lower bacterial and fungal diversity characterized higher altitude levels, along with a high proportion of shared bacterial (Thermoleophilia, Actinobacteria and Bacilli) and fungal (Eurotiomycetes and Mortierellomycota) taxa. Beech-dominated sites showed moderate soil quality and high bacterial (Alphaproteobacteria, Acidobacteria, Planctomycetes and Bacteroidetes) and fungal (Basidiomycota) diversity. Particularly, the Basidiomycota were well represented in pure beech forests at an altitude of 1500 m. In fertile and nitrogen rich soils with neutral pH, soil quality decreased along the altitudinal gradient, indicating that microbial diversity and forest floor decomposition were likely constrained by climatic conditions.

Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.

Response of a methane-driven interaction network to stressor intensification

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.

Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost. As permafrost thaws, research has shown that natural and anthropogenic soil disturbance causes microbial communities to undergo shifts in membership composition and biomass, as well as in functional diversity. Boreal forests are home to many plants that are integral to the subsistence diets of many Alaska Native communities. Yet, it is unclear how the observed shifts in soil microbes can affect above ground plant communities that are relied on as a major source of food. In this study, we tested the hypothesis that microbial communities associated with permafrost thaw affect plant productivity by growing five plant species found in Boreal forests and Tundra ecosystems, including low-bush cranberry and bog blueberry, with microbial communities from the active layer soils of a permafrost thaw gradient. We found that plant productivity was significantly affected by the microbial soil inoculants. Plants inoculated with communities from above thawing permafrost showed decreased productivity compared to plants inoculated with microbes from undisturbed soils. We used metagenomic sequencing to determine that microbial communities from disturbed soils above thawing permafrost differ in taxonomy from microbial communities in undisturbed soils above intact permafrost. The combination of these results indicates that a decrease in plant productivity can be linked to soil disturbance driven changes in microbial community membership and abundance. These data contribute to an understanding of how microbial communities can be affected by soil disturbance and climate change, and how those community shifts can further influence plant productivity in Boreal forests and more broadly, ecosystem health.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

Bacterial community dynamics in tropical soil after sewage sludge amendment

Although the widespread use of sewage sludge in developing countries is common, little is known about how sludge disposal can affect the microbial composition and diversity of tropical soils. We evaluated the effects of the sewage sludges of two types of anaerobic digestors differing, by the biological treatment they have undergone (uplow anaerobic sludge blanket and activated sludge digester), and two different disposal methods (surface and incorporated) on tropical soils. Samples were taken from topsoil (0-10 cm) and analyzed by amplifying the 16S rRNA genes to study the microbial community, and physicochemical analysis was performed concomitantly. The results indicated that, in general, sewage sludge amendment (SSA) significantly changed the tropical soil bacterial community by the sludge type and by application method. Moreover, the redundancy analysis diagram indicates that changes in soil chemical parameters over time due to SSA resulted in changes in the bacterial community's composition, increasing the population responsible for recycling nutrients in the soil.