Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River

Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments

Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.

16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L

Coffea sp. is cultivated in many tropical countries. Brazil has always adopted intensive agricultural practices, but organic coffee farming is an alternative system based on the non-use of agrochemicals and the rational management of soils. Metabarcoding 16S analysis using next-generation sequencing has been developed to identify and compare the diversity of the Coffea arabica L. rhizospheric bacterial community in two farming areas in São Paulo, Brazil. Dourado uses conventional farming, while Ribeirão Corrente uses organic. We found broad taxonomic composition, with sequences from 24 phyla, 55 classes, 61 orders, 146 families, and 337genus. The three most abundant phyla were Proteobacteria (38.27%), Actinobacteria (15.56%), and Acidobacteria (16.10%). In organic farming, the top 3 were the family Sphingomonadaceae, order Rhizobiales, genus Nocardioides, and Gp6. The genus Gp2 and the phylum Candidatus Saccharibacteria were the most abundant OTUs exclusively present in conventional farming. In the organic farming practice, Proteobacteria, Actinobacteria, and Acidobacteria were also present among the exclusive OTUs; we also found OTUs belonging to Bacteroidetes, Firmicutes, and Verrucomicrobia. Our study indicates a positive effect of organic farming on microbial communities. Fertilization may directly affect soil microbiota, suggesting that a large and active microbial community low in functional diversity might not adapt to new climatic conditions. A diverse community could provide better resilience to environmental changes, improving the productivity of this important crop.

Influence of organic plant breeding on the rhizosphere microbiome of common bean (Phaseolus vulgaris L.)

Introduction

We now recognize that plant genotype affects the assembly of its microbiome, which in turn, affects essential plant functions. The production system for crop plants also influences the microbiome composition, and as a result, we would expect to find differences between conventional and organic production systems. Plant genotypes selected in an organic regime may host different microbiome assemblages than those selected in conventional environments. We aimed to address these questions using recombinant inbred populations of snap bean that differed in breeding history.

Methods

Rhizosphere microbiomes of conventional and organic common beans (Phaseolus vulgaris L.) were characterized within a long-term organic research site. The fungal and bacterial communities were distinguished using pooled replications of 16S and ITS amplicon sequences, which originated from rhizosphere samples collected between flowering and pod set.

Results

Bacterial communities significantly varied between organic and conventional breeding histories, while fungal communities varied between breeding histories and parentage. Within the organically-bred populations, a higher abundance of a plant-growth-promoting bacteria, Arthrobacter pokkalii, was identified. Conventionally-bred beans hosted a higher abundance of nitrogen-fixing bacteria that normally do not form functional nodules with common beans. Fungal communities in the organically derived beans included more arbuscular mycorrhizae, as well as several plant pathogens.

Discussion

The results confirm that the breeding environment of crops can significantly alter the microbiome community composition of progeny. Characterizing changes in microbiome communities and the plant genes instrumental to these changes will provide essential information about how future breeding efforts may pursue microbiome manipulation.

Diversity and Functional Distribution Characteristics of Myxobacterial Communities in the Rhizosphere of Tamarix chinensis Lour in Ebinur Lake Wetland, China

Soil salinity and desertification are seriously threatening the ecological environment of Ebinur Lake Wetland. Myxobacteria are the main soil microbes in this wetland. However, it is still unclear if the myxobacterial community structure and diversity can improve the ecological environment of Ebinur Lake Wetland by regulating soil nutrient cycling. Therefore, based on high-throughput sequencing of 16SrRNA gene technology, the composition, function, and diversity of the myxobacterial community in the rhizosphere of Tamarix chinensis Lour in Ebinur Lake Wetland were studied. Rhizosphere soil samples were collected from 10 sampling sites (S1, S2, S3, S4, S5, S6, S7, S8, S9, and S10) for three months (April, July, and October) to explore the main biotic and abiotic factors affecting the diversity and functions of myxobacterial communities. The results revealed that diversity of myxobacterial communities was mainly influenced by the seasons. The diversity of myxobacterial communities was significantly higher in the month of July, as compared to April and October. FAPROTAX functional prediction revealed that, in addition to predation or parasitic functions, myxobacteria were mainly involved in ecological functions, such as nitrite respiration, nitrite ammonification, and nitrogen respiration. The Spearman correlation analysis of the diversity and function of myxobacteria and bacteria showed that there were significant positive correlations between myxobacteria diversity, function, and bacterial diversity. The co-occurrence analysis of myxobacteria and bacterial networks showed that over time, myxobacteria interacted differently with different bacterial networks and jointly regulated the microbial community in the rhizosphere of Tamarix chinensis Lour through predation or cooperation. The redundancy analysis of soil physicochemical factors as well as the myxobacterial community showed that electrical conductivity, exchangeable calcium, and exchangeable potassium were the most important abiotic factors affecting the diversity, structure, and function of the myxobacterial community. These results reveal that myxobacteria may play important roles in degrading nitrogen compounds and regulating the activity of soil microorganisms. This study provides theoretical support for the ecological restoration of Ebinur Lake Wetland and lays the foundation for the future development and utilization of myxobacteria resources.

Organic Farming Allows Balanced Fungal and Oomycetes Communities

Conventional and organic farming systems affect soils differently, thereby influencing microbial diversity and composition. Organic farming, which relies on natural processes, biodiversity, and cycles adapted to local conditions, is generally known to improve soil texture and alleviate microbial diversity loss compared with that of conventional farming, which uses synthetic inputs such as chemical fertilisers, pesticides, and herbicides. Although they affect the health and productivity of host plants, the community dynamics of fungi and fungi-like oomycetes (under Chromista) in organic farmland are poorly understood. The present study aimed to determine the differences in the diversity and composition of fungi and oomycetes inhabiting organic and conventional farm soils using culture-based DNA barcoding and culture-independent environmental DNA (eDNA) metabarcoding. Four tomato farms with different farming practices were selected and investigated: mature pure organic (MPO) via non-pesticide and organic fertiliser, mature integrated organic (MIO) via non-pesticide and chemical fertiliser, mature conventional chemical (MCC) via both pesticide and chemical fertiliser, and young conventional chemical (YCC). Culture-based analysis revealed that different genera were dominant on the four farms: Linnemannia in MPO, Mucor in MIO, and Globisporangium in MCC and YCC. eDNA metabarcoding demonstrated that the fungal richness and diversity on the MPO farm were higher than that on other farms. Both conventional farms exhibited simpler fungal and oomycete network structures with lower phylogenetic diversity. Interestingly, a high richness of oomycetes was shown in YCC; in which, Globisporangium, a potential pathogenic group on tomato plants, was abundantly observed. Our findings indicate that organic farming enhances fungal and oomycete diversity, which may provide robust support for maintaining healthy and sustainable agricultural practices. This study contributes to our knowledge on the positive effects of organic farming on crop microbiomes and provides essential information for maintaining biological diversity.

Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils

Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data

BACKGROUND

The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment.

RESULTS

This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B₁₂) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 .

CONCLUSIONS

This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest

Understanding plant-microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.

Temporal dynamics of total and active root-associated diazotrophic communities in field-grown rice

Plant-associated nitrogen-fixing microorganisms (diazotrophs) are essential to host nutrient acquisition, productivity and health, but how host growth affects the succession characteristics of crop diazotrophic communities is still poorly understood. Here, Illumina sequencing of DNA- and RNA-derived nifH genes was employed to investigate the dynamics of total and active diazotrophic communities across rhizosphere soil and rice roots under four fertilization regimes during three growth periods (tillering, heading and mature stages) of rice in 2015 and 2016. Our results indicated that 71.9–77.2% of the operational taxonomic units (OTUs) were both detected at the DNA and RNA levels. According to the nonmetric multidimensional scaling ordinations of Bray–Curtis distances, the variations in community composition of active rhizosphere diazotrophs were greater than those of total rhizosphere diazotrophs. The community composition (β-diversity) of total and active root-associated diazotrophs was shaped predominantly by microhabitat (niche; R² ≥ 0.959, p < 0.001), followed by growth period (R² ≥ 0.15, p < 0.001). The growth period had a stronger effect on endophytic diazotrophs than on rhizosphere diazotrophs. From the tillering stage to the heading stage, the α-diversity indices (Chao1, Shannon and phylogenetic diversity) and network topological parameters (edge numbers, average clustering coefficient and average degree values) of total endophytic diazotrophic communities increased. The proportions of OTUs shared by the total rhizosphere and endophytic diazotrophs in rhizosphere diazotrophs gradually increased during rice growth. Moreover, total diazotrophic α-diversity and network complexity decreased from rhizosphere soil to roots. Collectively, compared with total diazotrophic communities, active diazotrophic communities were better indicators of biological response to environmental changes. The host microhabitat profoundly drove the temporal dynamics of total and active root-associated diazotrophic communities, followed by the plant growth period.

Arbuscular Mycorrhizal Fungi and Dry Raw Garlic Stalk Amendment Alleviate Continuous Monocropping Growth and Photosynthetic Declines in Eggplant by Bolstering Its Antioxidant System and Accumulation of Osmolytes and Secondary Metabolites

Vegetable production under plastic sheds severely threatens regional eco-sustainability via anthropogenic activities (excessive use of agrochemicals, pesticides) and problems associated with replanting. Long-term successive cropping across growing seasons induces continuous cropping stress, whose effects manifest as diminished plant growth. Therefore, it is imperative that we develop environmentally sustainable approaches, such as replacing agrochemicals with vegetable waste like dry raw garlic stalk (DRGS) or use biofertilizers like arbuscular mycorrhizal fungi (AMF) (e.g., Diversispora epigaea). In this study, the influence of AMF on the growth, biochemical attributes, antioxidant defense system, phytohormones, accumulation of osmolytes, phenols, and mineral elements in eggplant grown on DRGS-amended soils under continuous monocropping (CMC) was studied. The results showed that inoculation with AMF or the DRGS amendment could improve the pigments' content, photosynthesis, and antioxidant defense system; augmented phytohormones synthesis (except for ABA), and increased the leaves' mineral nutrients. These parameters were enhanced most by the combined application of AMF and DRGS, which also increased the concentration of osmolytes, including proline, sugars, and free amino acids in eggplant when compared with the control. Furthermore, either AMF and DRGS alone, or in combination, ameliorated the induced stress from continuous cropping by reducing the incidence of Fusarium wilt and production of ROS (reactive oxygen species); lipid peroxidation underwent maximal reduction in plants grown under the combined treatments. The AMF, DRGS, and AMF + DRGS exhibited a lower disease severity index (33.46, 36.42, and 43.01%), respectively, over control. Hence, inoculation with AMF coupled with DRGS amendment alters the photosynthetic attributes in eggplant through the upregulation of its antioxidant system and greater accumulation of osmolytes, which led to the improved growth and yield of eggplant.

Soil Microbiomes in Apple Orchards Are Influenced by the Type of Agricultural Management but Never Match the Complexity and Connectivity of a Semi-natural Benchmark

Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.

Different soil salinity imparts clear alteration in rhizospheric bacterial community dynamics in rice and peanut

The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in the overall health of the hostplant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN, whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community structure is related to both the adjoining soil characters and the type of the hosts.

Isolation and characterization of plant growth promoting rhizobacteria isolated from organically grown high yielding pole type native pea (Pisum sativum L.) variety Dentami of Sikkim, India

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The present research showcases the significant findings pertaining to the assessment and report of the first ever study on the isolation and identification of plant growth promoting rhizobacterial diversity of organic farming pea variety (Dentami) of Sikkim. Proteobacteria dominated the rhizospheric soil whereas the bulk soil was governed by Actinobacteria. Bacillus cereus P8 (66.5 µg ml⁻¹) and Bacillus mycoides PP1 (45.1 µg ml⁻¹) were the highest IAA producer and also showed other plant growth promoting and biocontrol traits, such as phosphorous and potassium solubilization, nitrogen-fixing activity and siderophore production. As, Sikkim is the first state in India to practice organic agriculture farming, hence, such study on the soil microbiology is of immense significance. In these rhizospheric soil, it was dominated by the Proteobacteria and similar bacterial isolates, suggesting that these soil flora might be playing significant roles to enhancing the crop production and soil fertility.

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Culture-dependent technique was used to assess plant growth promoting rhizobacterial diversity of pole type pea variety (Dentami) of Sikkim.

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The dominant phylum was Proteobacteria (56%) from rhizosphere soil and Actinobacteria (58%) from bulk soil.

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PCA analysis showed that Firmicutes (bulk soil) were positively correlated to SOC, and available K, whereas, Proteobacteria (rhizosphere soil) exhibited a high correlation to pH, and available P.

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Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus UP1, and Bacillus mycoides PP1 showed plant growth promotion and bio-control traits.

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Bacillus cereus P8 (66.5 µg mL⁻¹) and Bacillus mycoides PP1 (45.1 µg mL⁻¹) was thehighest IAA producer.

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Pot experiment confirmed that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India.

Organic farming is an eco-friendly and sustainable farming practice that enhances soil fertility and helps in improving soil quality. But with the commencement of more sophisticated advances in agricultural techniques, organic farming has gradually become limited in the world. Culture-dependent plant growth-promoting bacterial isolates were isolated from the bulk and rhizospheric soil, of the native high yielding pole type organic pea (Pisum sativum L.) cultivar Dentami of Dentam, West Sikkim, India. Based on the 16S rRNA gene sequencing identification of these isolates, it was found that from the bulk soil, Actinobacteria (58%) was the dominant phyla followed by Firmicutes (28%), and Proteobacteria (14%). In the rhizospheric soil it was dominated by Proteobacteria (56%), followed by Firmicutes (33%), and Bacteriodetes (11%). A total of 40 bacterial isolates were initially screened for the plant growth-promoting (PGP) activity and out of them only four bacterial isolates i.e., Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus PP3, and Bacillus mycoides PP10 with accession numbers MN589697, MN559516, MN519462 and MN589696 respectively were found to possess higher PGP activity (i.e. phosphorous, potassium solubilization and nitrogen-fixing activity) as compared to the other bacteria present in the soil. Based on the indole-3-acetic acid (IAA) quantitative assay and siderophore production assay, it was found that Bacillus cereus (MN589697) produced the highest IAA (65.5 µg mL⁻¹) and siderophore (71%) when compared with the other isolates. The statistical correlation suggests that pH and available phosphorus were the strongest influencing factors for the distribution of Proteobacteria in the rhizospheric soil. The results indicate that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India. To the best of our knowledge the present study is the first report of its kind and showcases significant findings pertaining to the assessment of diversity, isolation and identification of plant growth-promoting rhizobacteria of organic pea grown in Sikkim.

Isolation and characterization of KDML105 aromatic rice rhizobacteria producing indole-3-acetic acid: impact of organic and conventional paddy rice practices

Indole-3-acetic acid (IAA) synthesis is a major property of rhizosphere bacteria. The IAA-producing ability of rhizobacteria may be influenced by agricultural management. We therefore evaluated the IAA-producing potential of rhizobacteria isolated during organic rice farming (ORF) and conventional rice farming (CRF) in Thung Kula Rong Hai areas of Thailand. The results indicated that ORF gave a significantly higher percentage of IAA producers (95·8%) than CRF (69·9%). The average IAA values of the ORF isolates were around two times higher than those of the CRF isolates both in the absence (12·8 and 5·8 μg IAA ml^-1 , respectively) and presence of L-tryptophan (L-Trp) (35·2 and 17·2 μg IAA ml^-1 , respectively). The 16S rRNA gene sequence analysis indicated that the 23 selected isolates belonged to 8 different genera-Sinomonas sp., Micrococcus sp., Microbacterium sp., Fictibacillus sp., Bacillus sp., Burkholderia sp., Leclercia sp. and Enterobacter sp. Interestingly, only three ORF isolates, i.e. ORF15-20 (Micrococcus sp.), ORF15-21 (Sinomonas sp.) and ORF15-23 (Sinomonas sp.), exhibited high IAA production ability without L-Trp (128·5, 160·8 and 174·7 μg IAA ml^-1 , respectively). Meanwhile, a slight decrease in IAA production with L-Trp was noticed, suggesting that the L-Trp was not used for the IAA synthesis of these isolates. Biopriming with rhizobacterial isolates significantly enhanced the rate of germination of KDML 105 rice seeds compared to the control.

Community Profile and Drivers of Predatory Myxobacteria under Different Compost Manures

Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the organic soil, which could be related to the presence of abundant myxobacteria in the applied compost manure during organic conditions. In the present study,16S rRNA genes sequencing technology was used to investigate the community profile and drivers of predatory myxobacteria in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (p < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg²⁺ and Ca²⁺ concentrations were the major factors influencing the myxobacteria community under different compost manure treatments. In addition, organic carbon, pH, and total nitrogen influenced the community profile of myxobacteria in compost manure. The interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure may explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ community profile of predatory myxobacteria and the key microorganism influencing their community would advance our understanding of the community profile and functions of predatory microorganisms in the microbial world.

Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

Variations in bacterial taxonomic profiles and potential functions in response to the gut transit of earthworms (Eisenia fetida) feeding on cow manure

Earthworms play an important role in the organic matter decomposition in terrestrial ecosystems. Earthworms interact directly with the microorganisms to affect the organic matter decomposition via gut transit, i.e., the digestion and assimilation of organic matter in the foregut and midgut and its excretion by the hindgut. However, how the microbial community ingested by earthworms respond to the transit processes in different gut segments of earthworms is not clear. We used composted cow manure to feed earthworms and sampled vermicompost and the contents of foregut, midgut and hindgut for bacterial 16S rRNA gene sequencing analysis. We observed that earthworm gut transit decreased the abundances of the dominant phyla Proteobacteria and Bacteroidetes but increased Actinobacteria, Chloroflexi and Acidobacteria. The alpha diversity of bacterial community in midgut was the lowest of the different gut segments, and the bacterial community structure of the foregut was significantly different from the midgut and hindgut. The enrichment analysis results revealed different selective stimulatory and inhibitory effects on the ingested bacterial community in the different gut segments, which extended to vermicompost. The FAPROTAX data indicated that C and N metabolic microbes were enriched in the earthworm gut. Microbes involved in fermentation and methanogenesis were enriched in the hindgut, and denitrification microbes were enriched in the foregut. The N metabolism microbes in vermicompost were significantly enriched after the stimulation of earthworm gut transit (P < 0.05), and the pathogenic microbes of animals and plants were inhibited. Combined with the results of subsequent correlation and biochemical analyses, earthworm gut transit significantly altered the structure and function of the bacterial community to accelerate the degradation and mineralization of organic matter and the enrichment of phosphorus and potassium. Our study suggests that the gut transit process of earthworms plays an important role in regulating organic matter dynamics in terrestrial ecosystems.

Effects of Abiotic Stress on Soil Microbiome

Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.

Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO₄ ^2-, SOC, HCO₃ ^-, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

Agricultural management practices influence the soil enzyme activity and bacterial community structure in tea plantations

BACKGROUND

The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period. Soil samples at two-months intervals were collected and analyzed.

RESULTS

The results of the enzyme activities revealed that acid phosphatase, arylsulfatase, β-glucosidase, and urease activities differed considerably among the soils representing the three management practices. Combining the redundancy and multiple regression analysis, the change in the arylsulfatase activity was explained by soil pH as a significant predictor in the SA soils. The soil bacterial community was predominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes in the soil throughout the sampling period. Higher Alpha diversity scores indicated increased bacterial abundance and diversity in the SA soils. A significant relationship between bacterial richness indices (SOBS, Chao and ACE) and soil pH, K and, P was observed in the SA soils. The diversity indices namely Shannon and Simpson also showed variations, suggesting the shift in the diversity of less abundant and more common species. Furthermore, the agricultural management practices, soil pH fluctuation, and the extractable elements had a greater influence on bacterial structure than that of temporal change.

CONCLUSIONS

Based on the cross-over analysis of the bacterial composition, enzymatic activity, and soil properties, the relationship between bacterial composition and biologically-driven ecological processes can be identified as indicators of sustainability for the tea plantation.

Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits

A nature farming system is an ecological farming practice that entails cultivating crops without using chemical fertilizers and pesticides. To understand the diversity and functions of root microbiomes associated with nature farming systems, we compared the root microbial community of rice under nature farming conditions with those under conventional farming conditions. High-throughput amplicon analysis demonstrated a higher abundance and greater diversity of the root microbiome under unfertilized nature farming conditions than under conventional conditions. The application of chemical fertilizers reduced the microbial diversity and abundance of some beneficial taxa important for plant growth and health. Subsequently, we isolated and identified 46 endo- and epiphytic bacteria from rice roots grown under nature farming conditions and examined their plant growth-promoting activity. Six potential isolates were selected for plant growth assessment in insoluble P- and K-containing media. Most of the isolates promoted rice growth, and Pseudomonas koreensis AEPR1 was able to enhance rice growth significantly in both insoluble P- and K-containing media. Our data indicated that nature farming systems create a distinct root microbiome that is comparatively more diverse and supports plant growth under low-input cultivation practices than under conventional practices. The potential isolates could be exploited as sources with potential applications in sustainable agriculture.

Wine Terroir and the Soil Bacteria: An Amplicon Sequencing-Based Assessment of the Barossa Valley and Its Sub-Regions

A wines' terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

Response of Horticultural Soil Microbiota to Different Fertilization Practices

Environmentally friendly agricultural production necessitates manipulation of microbe-plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.

Structural and functional microbial diversity of sandy soil under cropland and grassland

Background

Land use change significantly alters soil organic carbon content and the microbial community. Therefore, in the present study, the effect of changing cropland to grassland on structural and functional soil microbial diversity was evaluated. The specific aims were (i) to identify the most prominent members of the fungal communities and their relevant ecological guild groups; (ii) to assess changes in the diversity of ammonia-oxidizing archaea; (iii) to determine the relationships between microbial diversity and selected physical and chemical properties.

Methods

We investigated microbial diversity and activity indicators, bulk density and the water-holding capacity of sandy soil under both cropland and 25-year-old grassland (formerly cropland) in Trzebieszów, in the Podlasie Region, Poland. Microbial diversity was assessed by: the relative abundance of ammonia-oxidizing archaea, fungal community composition and functional diversity. Microbial activity was assessed by soil enzyme (dehydrogenase, β-glucosidase) and respiration tests.

Results

It was shown that compared to cropland, grassland has a higher soil organic carbon content, microbial biomass, basal respiration, rate of enzyme activity, richness and diversity of the microbial community, water holding capacity and the structure of the fungal and ammonia-oxidizing archaea communities was also altered. The implications of these results for soil quality and soil health are also discussed. The results suggest that grassland can have a significant phytosanitary capacity with regard to ecosystem services, due to the prominent presence of beneficial and antagonistic microbes. Moreover, the results also suggest that grassland use may improve the status of soil organic carbon and nitrogen dynamics, thereby increasing the relative abundance of fungi and ammonia-oxidizing archaea.

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition

Rice (Oryza sativa. L) has been intensively studied to ensure a stable global supply of this commodity in the face of rapid global climate change. A critical factor that decreases crop yield is drought, which has been analyzed in various ways through many researches. Microbiome-based studies of rice investigate the symbiosis between rice and bacteria, which has been proposed as a way to overcome problems caused by drought. Several rice-associated metagenomic profiles obtained under drought conditions have been reported since the advent of next generation sequencing (NGS) technology. To elucidate the future diversity of plants and microorganisms and to promote sustainable agriculture, we reanalyzed 64 of the publicly available 16S amplicon sequencing data produced under drought condition. In the process of integrating data sets, however, we found an inconsistency that serves as a bottleneck for microbiome-based sustainability research. While this report provides clues about the composition of the microbiome under the drought conditions, the results are affected by differences in the location of the experiments, sampling conditions, and analysis protocols. Re-analysis of amplicon sequencing data of the soil microbiome in rice fields suggests that microbial composition shifts in response to drought condition and the presence of plants. Among the bacteria involved, the phylum Proteobacteria appears to play the most important role in the survival of rice under drought condition.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community

BACKGROUND

Myxobacteria are micropredators in the soil ecosystem with the capacity to move and feed cooperatively. Some myxobacterial strains have been used to control soil-borne fungal phytopathogens. However, interactions among myxobacteria, plant pathogens, and the soil microbiome are largely unexplored. In this study, we aimed to investigate the behaviors of the myxobacterium Corallococcus sp. strain EGB in the soil and its effect on the soil microbiome after inoculation for controlling cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (FOC).

RESULTS

A greenhouse and a 2-year field experiment demonstrated that the solid-state fermented strain EGB significantly reduced the cucumber Fusarium wilt by 79.6% (greenhouse), 66.0% (2015, field), and 53.9% (2016, field). Strain EGB adapted to the soil environment well and decreased the abundance of soil-borne FOC efficiently. Spatiotemporal analysis of the soil microbial community showed that strain EGB migrated towards the roots and root exudates of the cucumber plants via chemotaxis. Cooccurrence network analysis of the soil microbiome indicated a decreased modularity and community number but an increased connection number per node after the application of strain EGB. Several predatory bacteria, such as Lysobacter, Microvirga, and Cupriavidus, appearing as hubs or indicators, showed intensive connections with other bacteria.

CONCLUSION

The predatory myxobacterium Corallococcus sp. strain EGB controlled cucumber Fusarium wilt by migrating to the plant root and regulating the soil microbial community. This strain has the potential to be developed as a novel biological control agent of soil-borne Fusarium wilt. Video abstract.

Long-term nitrogen application decreases the abundance and copy number of predatory myxobacteria and alters the myxobacterial community structure in the soil

Myxobacteria are fascinating micro-predators due to their extraordinary social lifestyle, which is unique in the bacterial domain. These taxa are metabolically active in the soil microbial food web and control populations of soil microbes. However, the effects of fertilisation treatments on predatory myxobacteria in agricultural systems are often overlooked. Here, the high-throughput absolute abundance quantification (HAAQ) method was employed to investigate the abundance and cell density of myxobacteria in the Red Soil Experimental Station fields following 29 years of fertilisation. Using 16S rRNA gene amplicons, we detected a total of 419 myxobacterial operational taxonomic units (OTUs), accounting for 0.25-2.70% of the total bacterial abundance. Significantly different myxobacterial communities were found between nitrogen-fertilised (N_cluster) and manure-fertilised (M_cluster) samples by principal coordinate analysis (PCoA), analysis of similarities (ANOSIM), and Manhattan analysis (p < 0.05). N fertiliser treatments significantly decreased the myxobacterial abundance and copy number, species accumulation index (S), and Shannon index (p < 0.05). Furthermore, UpSet plots showed that the OTU number in the N fertiliser treatment was only 24.4% of that in the M treatment, as the application of N decreased the number of low-abundance myxobacterial OTUs. In addition, network analysis, redundancy analysis (RDA), and random forest (RF) analysis showed that myxobacterial abundance and copy number were the most important variables predicting the soil bacterial community and functional gene α- and β-diversity (P < 0.05). Our findings imply that soil acidification caused by the application of nitrogen fertilisers is the most important driver of the decrease in the myxobacterial abundance and copy number in the soil. We suggest that the changes in the abundance and number of myxobacteria are strongly correlated with the overall bacterial α- and β-diversity indices. In addition, such changes may be an important factor in the overall changes in microbial communities.

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products

The mung bean has a great potential under tropical conditions given its high content of grain protein. Additionally, its ability to benefit from biological nitrogen fixation (BNF) through association with native rhizobia inhabiting nodule microbiome provides most of the nitrogen independence on fertilizers. Soil microbial communities which are influenced by biogeographical factors and soil properties, represent a source of rhizobacteria capable of stimulating plant growth. The objective of this study is to support selection of beneficial bacteria that form positive interactions with mung bean plants cultivated in tropical soils, as part of a seed inoculation program for increasing grain yield based on the BNF and other mechanisms. Two mung bean genotypes (Camaleão and Esmeralda) were cultivated in 10 soil samples. Nodule microbiome was characterized by next-generation sequencing using Illumina MiSeq 16S rRNA. More than 99% of nodule sequences showed similarity with Bradyrhizobium genus, the only rhizobial present in nodules in our study. Higher bacterial diversity of soil samples collected in agribusiness areas (MW_MT-I, II or III) was associated with Esmeralda genotype, while an organic agroecosystem soil sample (SE_RJ-V) showed the highest bacterial diversity independent of genotype. Furthermore, OTUs close to Bradyrhizobium elkanii have dominated in all soil samples, except in the sample from the organic agroecosystem, where just B. japonicum was present. Bacterial community of mung bean nodules is mainly influenced by soil pH, K, Ca, and P. Besides a difference on nodule colonization by OTU sequences close to the Pseudomonas genus regarding the two genotypes was detected too. Although representing a small rate, around 0.1% of the total, Pseudomonas OTUs were only retrieved from nodules of Esmeralda genotype, suggesting a different trait regarding specificity between macro- and micro-symbionts. The microbiome analysis will guide the next steps in the development of an inoculant for mung bean aiming to promote plant growth and grain yield, composed either by an efficient Bradyrhizobium strain on its own or co-inoculated with a Pseudomonas strain. Considering the results achieved, the assessment of microbial ecology parameters is a potent coadjuvant capable to accelerate the inoculant development process and to improve the benefits to the crop by soil microorganisms.

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

BACKGROUND

Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.

RESULTS

Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.

CONCLUSIONS

Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.

The metagenomic landscape of xenobiotics biodegradation in mangrove sediments

Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.

Tree Species Shape Soil Bacterial Community Structure and Function in Temperate Deciduous Forests

Amplicon-based analysis of 16S rRNA genes and transcripts was used to assess the effect of tree species composition on soil bacterial community structure and function in a temperate deciduous forest. Samples were collected from mono and mixed stands of Fagus sylvatica (beech), Carpinus betulus (hornbeam), Tilia sp. (lime), and Quercus sp. (oak) in spring, summer, and autumn. Soil bacterial community exhibited similar taxonomic composition at total (DNA-based) and potentially active community (RNA-based) level, with fewer taxa present at active community level. Members of Rhizobiales dominated at both total and active bacterial community level, followed by members of Acidobacteriales, Solibacterales, Rhodospirillales, and Xanthomonadales. Bacterial communities at total and active community level showed a significant positive correlation with tree species identity (mono stands) and to a lesser extent with tree species richness (mixed stands). Approximately 58 and 64% of indicator operational taxonomic units (OTUs) showed significant association with only one mono stand at total and active community level, respectively, indicating a strong impact of tree species on soil bacterial community composition. Soil C/N ratio, pH, and P content similarly exhibited a significant positive correlation with soil bacterial communities, which was attributed to direct and indirect effects of forest stands. Seasonality was the strongest driver of predicted metabolic functions related to C fixation and degradation, and N metabolism. Carbon and nitrogen metabolic processes were significantly abundant in spring, while C degradation gene abundances increased from summer to autumn, corresponding to increased litterfall and decomposition. The results revealed that in a spatially homogenous forest soil, tree species diversity and richness are dominant drivers of structure and composition in soil bacterial communities.

Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.

Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

Succession of Composition and Function of Soil Bacterial Communities During Key Rice Growth Stages

Elucidating the succession of soil microbial communities and microbial functions at key plant growth stages is a major goal of microbial ecology research. In this study, we investigated the succession of soil bacteria during four fertilizer treatments (control, NPK, NPK + pig manure, and NPK + straw) and at three crucial rice growth stages (tillering, heading, and ripening) in paddy soil from a rice-wheat cropping system over a 10-year period. The results showed that the bacterial community and function composition of the control treatment was significantly different from that of the other treatments with NPK fertilizers, and S1 from others stages (ANOSIM, p < 0.05). The application of pig manure could reduce the effects of applying NPK fertilizers on bacterial communities in heading and ripening stages, but the effects of straw returning is not obvious. Variance partitioning analyses (VPA) suggested that pH, OM, and AK appeared to be key factors responsible for the microbial community changes observed in all the treatments or stages. The correlation results showed the bacterial families different between S1 and other stages such as Micromonosporaceae, Nocardioidaceae, Gaiellaceae, and Anaerolineaceae etc., were correlated with bacterial KEGG metabolic pathways. In addition, the topological of the soil bacterial community network with more nodes, links and higher Maximal degree at the heading stage and maintained relatively similar topological structures at the heading and ripening stages. However, the topological of the functional networks at the ripening stage were a small yet complicated co-occurring network with 209 nodes, 789 links, higher Average connectivity (avgK), and Maximal degree. These results suggest an obvious succession of soil bacteria and bacterial function at the key rice growth stages, but the topological of functional network structure of bacteria changes a little in the early and middle stages of rice, while its changes significantly in the ripening stage of rice growth.

Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

Agricultural practices have significant impacts on soil properties and microbial communities; however, little is known about their responses to open field and plastic tunnels under organic and conventional farming. We therefore investigated the responses of soil chemical variables and microbial communities to different agricultural management and cultivation types, including organic management in open field (OF), organic management in plastic tunnels (OP), conventional management in open field (CF) and conventional management in plastic tunnels (CP), by using a pyrosequencing approach of 16S rRNA gene amplicon. Both factors had significant influences on the soil properties and microbial communities. Organic farming increased the nutrient-related soil variables compared to conventional farming regardless of cultivation type, especially for the available N and P, which were increased by 137% and 711%, respectively, in OP compared to CP. Additionally, OP had the highest microbial abundance and diversity among treatments, whereas no difference was found between OF, CF and CP. Furthermore, OP possessed diverse differential bacteria which were mainly related to the organic material turnover (e.g., Roseiflexus, Planctomyces and Butyrivibrio) and plant growth promotion (e.g., Nostoc, Glycomyces and Bacillus). Redundancy analysis (RDA) showed that pH, electrical conductivity (EC), nutrient levels (e.g., available N and available P) and total Zn content were significantly correlated to the structure of the microbial community. Overall, our results showed that the long-term organic farming with high fertilizer input increased soil nutrient levels and microbial abundance and diversity under plastic-tunnel condition compared to other cultivation systems.

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil

Soil productivity is strongly influenced by the activities of microbial communities. However, it is not well understood how community structure, including its richness, mass, and composition, influences soil functions. We investigated the relationships between soil productivity and microbial communities in unfertilized arable soils extending over 1000 km in eastern Japan. Soil properties, including C turnover rate, N mineralization rate, microbial C, and various soil chemical properties, were measured. Soil bacterial and fungal communities were analyzed by Illumina's MiSeq using 16S rRNA and ITS regions. In addition, root microbial communities from maize grown in each soil were also investigated. Soil bacterial communities shared many operational taxonomic units (OTUs) among farms. An ordination plot based on correspondence analysis revealed convergent distribution of soil bacterial communities across the farms, which seemed to be a result of similar agricultural management practices. Although fungal communities showed lower richness and a lower proportion of shared OTUs than bacterial communities, community structure between the farms tended to be convergent. On the other hand, root communities had lower richness and a higher abundance of specific taxa than the soil communities. Two soil functions, decomposition activity and soil productivity, were extracted by principal component analysis (PCA) based on eight soil properties. Soil productivity correlated with N mineralization rate, P2O5, and maize growth, but not with decomposition activity, which is characterized by C turnover rate, soil organic C, and microbial mass. Soil productivity showed a significant association with community composition, but not with richness and mass of soil microbial communities. Soil productivity also correlated with the abundance of several specific taxa, both in bacteria and fungi. Root communities did not show any clear correlations with soil productivity. These results demonstrate that community composition and abundance of soil microbial communities play important roles in determining soil productivity.

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations

Fertilization has a large impact on the soil microbial communities, which play pivotal roles in soil biogeochemical cycling and ecological processes. While the effects of changes in nutrient availability due to fertilization on the soil microbial communities have received considerable attention, specific microbial taxa strongly influenced by long-term organic and inorganic fertilization, their potential effects and associations with soil nutrients remain unclear. Here, we use deep 16S amplicon sequencing to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics (manure and straw)-inorganic fertilizers, and uncover potential links between soil nutrient parameters and specific bacterial taxa. Our results showed that combined organic-inorganic fertilization increased soil organic carbon (SOC) and total nitrogen (TN) contents and altered bacterial community composition, while inorganic fertilization had little impact on soil nutrients and bacterial community composition. SOC and TN emerged as the major determinants of community composition. The abundances of specific taxa, especially Arenimonas, Gemmatimonas, and an unclassified member of Xanthomonadaceae, were substantially increased by organic-inorganic amendments rather than inorganic amendments only. A co-occurrence based network analysis demonstrated that SOC and TN had strong positive associations with some taxa (Gemmatimonas and the members of Acidobacteria subgroup 6, Myxococcales, Betaproteobacteria, and Bacteroidetes), and Gemmatimonas, Flavobacterium, and an unclassified member of Verrucomicrobia were identified as the keystone taxa. These specific taxa identified above are implicated in the decomposition of complex organic matters and soil carbon, nitrogen, and phosphorus transformations. The present work strengthens our current understanding of the soil microbial community structure and functions under long-term fertilization management and provides certain theoretical support for selection of rational fertilization strategies.