Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

Interactive effects of microplastics and cadmium on soil properties, microbial communities and bok choy growth

The simultaneous presence of microplastics (MPs) and cadmium (Cd) in soil environments has raised concerns regarding their potential interactive effects on soil-plant ecosystems. This study explores how polyethylene (PE) at concentrations of 0.5 % (w/w), 1 % (w/w), and 2 % (w/w), and Cd at concentrations of 3 mg kg-1 and 12 mg kg-1, either alone or combined, impact soil physicochemical properties, microbial community structures, and bok choy growth through a 40-day pot experiment. Our findings reveal that the addition of 2 % (w/w) PE significantly increased soil organic carbon (SOC). However, when 2 % PE coexisted with Cd, SOC levels decreased, potentially due to a reduction in enzyme activity (β-1,4-glucosidase). PE increased the proportion of 1-2 mm soil aggregates, while the coexistence of 2 % PE and Cd significantly increased the content of soil aggregates larger than 2 mm. The coexistence of PE and Cd increased available potassium (AK) in the soil by approximately 13 % to 41 %. Regarding bok choy growth, the aboveground biomass under 2 % PE was approximately 210 % of that under 0.5 % PE, possibly because of the enhancement in soil nutrients. The presence of Cd, however, reduced the chlorophyll content of bok choy by approximately 18 % to 34 %. Notably, the coexistence of high PE concentration (2 % w/w) and low Cd concentration (3 mg kg-1) resulted in the highest aboveground biomass among all coexistence treatments. Furthermore, the addition of PE and Cd significantly altered the structure of soil bacterial and fungal communities, with fungi showing a greater response. Bacteria were significantly associated with soil inorganic N content and plant growth. This study provides new insights into the interactions of microplastics and Cd within microbial-soil-plant systems.

Effects of manure and nitrogen fertilization on soil microbial carbon fixation genes and associated communities in the Loess Plateau of China

The effects of long-term fertilization on soil carbon (C) cycling have been a key focus of agricultural sustainable development research. However, the influences of different fertilization treatments on soil microbial C fixation profiles are still unclear. Metagenomics technology and multivariate analysis were employed to inquire changes in soil properties, soil microbial C fixation genes and associated bacterial communities, and the influence of dominant soil properties on C fixation genes. The contents of soil C and nitrogen fractions were signicficantly higher in manure or combined with nitrogen fertilization (NM) than other treatments. The composition of soil microbial C fixation genes and associated bacterial communities varied among different fertilization treatments. Compared with other treatments, the total abundance of microbial C fixation genes and the abundance of Proteobacteria were significantly higher in NM than in other treatments, as well as the abundances of C fixation genes involved in dicarboxylate/4-hydroxybutyrate cycle and reductive citrate cycle. Key functional genes and main bacterial communities presented in the middle of the co-occurrence network. Soil organic carbon, total nitrogen, and microbial biomass nitrogen were the dominant soil properties influencing microbial C fixation genes and associated bacterial communitis. Fertilization increased the abundance of C fixation genes by affecting the changes in bacterial communities abundance mediated by soil properties. Overall, elucidating the responses of soil microbial C fixation genes and associated communities to different fertilization will enhance our understanding of the processes of soil C fixation in farmland.

Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities

Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.

Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems

Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)-cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.

Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

Differential impacts of polyethylene microplastic and additives on soil nitrogen cycling: A deeper dive into microbial interactions and transformation mechanisms

The impact of microplastics and their additives on soil nutrient cycling, particularly through microbial mechanisms, remains underexplored. This study investigated the effects of polyethylene microplastics, polyethylene resin, and plastic additives on soil nitrogen content, physicochemical properties, nitrogen cycling functional genes, microbial composition, and nitrogen transformation rates. Results showed that all amendments increased total nitrogen but decreased dissolved total nitrogen. Polyethylene microplastics and additives increased dissolved organic nitrogen, while polyethylene resin reduced it and exhibited higher microbial biomass. Amendments reduced or did not change inorganic nitrogen levels, with additives showing the lowest values. Polyethylene resin favored microbial nitrogen immobilization, while additives were more inhibitory. Amendment type and content significantly interacted with nitrogen cycling genes and microbial composition. Distinct functional microbial biomarkers and network structures were identified for different amendments. Polyethylene microplastics had higher gross ammonification, nitrification, and immobilization rates, followed by polyethylene resin and additives. Nitrogen transformation was driven by multiple functional genes, with Proteobacteria playing a significant role. Soil physicochemical properties affected nitrogen content through transformation rates, with C/N ratio having an indirect effect and water holding capacity directly impacting it. In summary, plastic additives, compared to polyethylene microplastics and resin, are less conducive to nitrogen degradation and microbial immobilization, exert significant effects on microbial community structure, inhibit transformation rates, and ultimately impact nitrogen cycling.

The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau

The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.

Effects of returning peach branch waste to fields on soil carbon cycle mediated by soil microbial communities

In recent years, the rise in greenhouse gas emissions from agriculture has worsened climate change. Efficiently utilizing agricultural waste can significantly mitigate these effects. This study investigated the ecological benefits of returning peach branch waste to fields (RPBF) through three innovative strategies: (1) application of peach branch organic fertilizer (OF), (2) mushroom cultivation using peach branches as a substrate (MC), and (3) surface mulching with peach branches (SM). Conducted within a peach orchard ecosystem, our research aimed to assess these resource utilization strategies' effects on soil properties, microbial community, and carbon cycle, thereby contributing to sustainable agricultural practices. Our findings indicated that all RPBF treatments enhance soil nutrient content, enriching beneficial microorganisms, such as Humicola, Rhizobiales, and Bacillus. Moreover, soil AP and AK were observed to regulate the soil carbon cycle by altering the compositions and functions of microbial communities. Notably, OF and MC treatments were found to boost autotrophic microorganism abundance, thereby augmenting the potential for soil carbon sequestration and emission reduction. Interestingly, in peach orchard soil, fungal communities were found to contribute more greatly to SOC content than bacterial communities. However, SM treatment resulted in an increase in the presence of bacterial communities, thereby enhancing carbon emissions. Overall, this study illustrated the fundamental pathways by which RPBF treatment affects the soil carbon cycle, providing novel insights into the rational resource utilization of peach branch waste and the advancement of ecological agriculture.

Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration

Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.

The Impact of Aboveground Epichloë Endophytic Fungi on the Rhizosphere Microbial Functions of the Host Melica transsilvanica

In nature, the symbiotic relationship between plants and microorganisms is crucial for ecosystem balance and plant growth. This study investigates the impact of Epichloë endophytic fungi, which are exclusively present aboveground, on the rhizosphere microbial functions of the host Melica transsilvanica. Using metagenomic methods, we analyzed the differences in microbial functional groups and functional genes in the rhizosphere soil between symbiotic (EI) and non-symbiotic (EF) plants. The results reveal that the presence of Epichloë altered the community structure of carbon and nitrogen cycling-related microbial populations in the host's rhizosphere, significantly increasing the abundance of the genes (porA, porG, IDH1) involved in the rTCA cycle of the carbon fixation pathway, as well as the abundance of nxrAB genes related to nitrification in the nitrogen-cycling pathway. Furthermore, the presence of Epichloë reduces the enrichment of virulence factors in the host rhizosphere microbiome, while significantly increasing the accumulation of resistance genes against heavy metals such as Zn, Sb, and Pb. This study provides new insights into the interactions among endophytic fungi, host plants, and rhizosphere microorganisms, and offers potential applications for utilizing endophytic fungi resources to improve plant growth and soil health.

Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO2 fixation pathways in coastal saline soil

Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.

Alterations in the composition and metabolite profiles of the saline-alkali soil microbial community through biochar application

Saline-alkali soil poses significant chanllenges to sustainable development of agriculture. Although biochar is commonly used as a soil organic amendment, its microbial remediation mechanism on saline-alkali soil requires further confirmation. To address this, we conducted a pot experiment using cotton seedlings to explore the potential remediation mechanism of rice straw biochar (BC) at three different levels on saline-alkaline soil. The results showed that adding of 2% biochar greatly improved the quality of saline-alkaline soil by reducing pH levels, electrical conductivity (EC), and water-soluble ions. Moreover, biochar increased the soil organic matter (SOM), nutrient availability and extracellular enzyme activity. Interestingly, it also reduced soil salinity and salt content in various cotton plant tissues. Additionally, biochar had a notable impact on the composition of the microbial community, causing changes in soil metabolic pathways. Notably, the addition of biochar promoted the growth and metabolism of dominant salt-tolerant bacteria, such as Proteobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota. By enhancing the positive correlation between microorganisms and metabolites, biochar alleviated the inhibitory effect of salt ions on microorganisms. In conclusion, the incorporation of biochar significantly improves the soil microenvironment, reduces soil salinity, and shows promise in ameliorating saline-alkaline soil conditions.

Metagenomic and genomic analysis of heavy metal-tolerant and -resistant bacteria in resource islands in a semi-arid zone of the Colombian Caribbean

Bacteria from resource islands can adapt to different extreme conditions in semi-arid regions. We aimed to determine the potential resistance and tolerance to heavy metals from the bacterial community under the canopy of three resource islands in a semi-arid zone of the Colombian Caribbean. Total DNA was extracted from soil and through a metagenomics approach, we identified genes related to heavy metal tolerance and resistance under the influence of drought and humidity conditions, as well as the presence or absence of vegetation. We characterized the genomes of bacterial isolates cultivated in the presence of four heavy metals. The abundances of genes related to heavy metal resistance and tolerance were favored by soil moisture and the presence of vegetation. We observed a high abundance of resistance genes (60.4%) for Cu, Zn, and Ni, while 39.6% represented tolerance. These genes positively correlated with clay and silt content, and negatively correlated with sand content. Resistance and tolerance were associated with detoxification mechanisms involving oxidoreductase enzymes, metalloproteases, and hydrolases, as well as transmembrane proteins involved in metal transport such as efflux pumps and ion transmembrane transporters. The Bacillus velezensis C3-3 and Cytobacillus gottheilii T106 isolates showed resistance to 5 mM of Cd, Co, Mn, and Ni through detoxification genes associated with ABC pumps, metal transport proteins, ion antiporter proteins, and import systems, among others. Overall, these findings highlight the potential of bacteria from resource islands in bioremediation processes of soils contaminated with heavy metals.

Microecological Shifts in the Rhizosphere of Perennial Large Trees and Seedlings in Continuous Cropping of Poplar

The cultivation of poplar trees is hindered by persistent cropping challenges, resulting in reduced wood productivity and increased susceptibility to soil-borne diseases. These issues primarily arise from alterations in microbial structure and the infiltration of pathogenic fungi. To investigate the impact on soil fertility, we conducted an analysis using soil samples from both perennial poplar trees and three successive generations of continuously cropped poplar trees. The quantity and community composition of bacteria and fungi in the rhizosphere were assessed using the Illumina MiSeq platform. The objective of this study is to elucidate the impact of continuous cropping challenges on soil fertility and rhizosphere microorganisms in poplar trees, thereby establishing a theoretical foundation for investigating the mechanisms underlying these challenges. The study found that the total bacteria in the BT group is 0.42 times higher than the CK group, and the total fungi is 0.33 times lower than the CK group. The BT and CK groups presented relatively similar bacterial richness and diversity, while the indices showed a significant (p < 0.05) higher fungal richness and diversity in the CK group. The fractions of Bacillus were 2.22% and 2.41% in the BT and CK groups, respectively. There was a 35.29% fraction of Inocybe in the BT group, whereas this was barely observed in the CK group. The fractions of Geopora were 26.25% and 5.99%, respectively in the BT and CK groups. Modifying the microbial community structure in soil subjected to continuous cropping is deemed as the most effective approach to mitigate the challenges associated with this agricultural practice.

Effect of flumetsulam alone and coexistence with polyethylene microplastics on soil microbial carbon and nitrogen cycles: Elucidation of bacterial community structure, functional gene expression, and enzyme activity

Flumetsulam (FLU) is a new class of broad-spectrum herbicides. With the widespread use of plastic products, polyethylene (PE) microplastics (MPs) may remain in the soil. It is possible for these two novel contaminants to co-exist in the soil environment. In the present study, we used brown soil as the test soil and determined the toxicity of FLU at 0.05, 0.5 and 2.5 mg kg-1 alone and in combination with PE MPs (1%) on soil microorganisms. The obtained results demonstrated that the exposure of FLU and FLU+MPs had an inhibitory effect on the numbers of bacteria and fungi. In addition, FLU and FLU+MPs caused changes in the relevant functional bacterial genera, favored nitrogen fixation and denitrification, and promoted soil carbon fixation, but inhibited nitrification. Compared to FLU exposure alone, exposure to FLU+MPs gave rise to significant differences in soil bacterial community composition, but did not affect carbon and nitrogen cycling. The integrated biomarker response results indicated that the toxicity of FLU and FLU+MPs to soil microorganisms increased with increasing concentrations of FLU. The present experiment clarified the toxicological effects of co-exposure of FLU and MPs on microorganisms and filled the toxicological data gap of FLU.

Efficient nitrogen removal pathways and corresponding microbial evidence in tidal flow constructed wetlands for saline water treatment

The artificial tidal wetlands ecosystem was believed to be a useful device in treating saline water, and it played a significant part in global nitrogen cycles. However, limited information is available on nitrogen-cycling pathways and related contributions to nitrogen loss in tidal flow constructed wetlands (TF-CWs) for saline water treatment. This study operated seven experimental tidal flow constructed wetlands to remove nitrogen from saline water at salinities of 0-30‰. Stable and high NH4+-N removal efficiency (∼90.3%) was achieved, compared to 4.8-93.4% and 23.5-88.4% for nitrate and total nitrogen (TN), respectively. Microbial analyses revealed the simultaneous occurrence of anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), nitrification and denitrification, contributing to nitrogen (N) loss from the mesocosms. The absolute abundances were 5.54 × 103-8.35 × 107 (nitrogen functional genes) and 5.21 × 107-7.99 × 109 copies/g (16S rRNA), while the related genera abundances ranged from 1.81% to 10.47% (nitrate reduction) and from 0.29% to 0.97% (nitrification), respectively. Quantitative response relationships showed ammonium transformation were controlled by nxrA, hzsB and amoA, and nitrate removal by nxrA, nosZ and narG. Collectively, TN transformation were determined by narG, nosZ, qnorB, nirS and hzsB through denitrification and anammox pathways. The proportion of nitrogen assimilation by plants was 6.9-23.4%. In summary, these findings would advance our understanding of quantitative molecular mechanisms in TF-CW mesocosms for treating nitrogen pollution that caused algal blooms in estuarine/coastal ecosystems worldwide.

Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas

Soil microbiota, which plays a fundamental role in ecosystem functioning, is sensitive to environmental changes. Studying soil microbial ecological patterns can help to understand the consequences of environmental disturbances on soil microbiota and hence ecosystem services. The different habitats with critical environmental gradients generated through the restoration of coal-mining subsidence areas provide an ideal area to explore the response of soil microbiota to environmental changes. Here, based on high-throughput sequencing, we revealed the patterns of soil bacterial and fungal communities in habitats with different land-use types (wetland, farmland, and grassland) and with different restored times which were generated during the ecological restoration of a typical coal-mining subsidence area in Jining City, China. The α-diversity of bacterial was higher in wetland than in farmland and grassland, while that of fungi had no discrepancy among the three habitats. The β-diversity of bacterial community in the grassland was lower than in the farmland, and fungal community was significant different in all three habitats, showing wetland, grassland, and farmland from high to low. The β-diversity of the bacterial community decreased with restoration time while that of the fungal community had no significant change in the longer-restoration-time area. Furthermore, soil electrical conductivity was the most important driver for both bacterial and fungal communities. Based on the taxonomic difference among different habitats, we identified a group of biomarkers for each habitat. The study contributes to understand the microbial patterns during the ecological restoration of coal-mining subsidence areas, which has implications for the efficient ecological restoration of subsidence areas.

Straw mulch improves soil carbon and nitrogen cycle by mediating microbial community structure and function in the maize field

This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, protease, and amylase activity. Overall, our findings imply that straw mulch might influence the bacterial and fungal community structures, thereby boosting the production of labile C and N components and accelerating the C and N cycle in maize fields.

Effects of nitrogen reduction combined with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard

Understanding soil bacterial diversity under nitrogen reduction is necessary for the crucial role in soil nitrogen cycling. However, the effects of combined fertilization on soil chemical properties, microbial community structure, and yield are unknown. This study was conducted to investigate the effect of nitrogen fertilizer reduction with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard. Six treatments were set in this study: NF-100%, NF-75%, NF-50%, NF-25% and CF, no nitrogen fertilizer and bio-organic fertilizer for CK. The bacterial community structures of soil were analyzed by 16S rRNA gene amplification high-throughput sequencing technology. Nitrogen fertilizer reduction with bio-organic fertilizer increased soil organic matter (SOM), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), available potassium (AK), and reduced soil pH. NF-50% and NF-25% treatments increased the yield of red raspberry. Nitrogen reduction combined with bio-organic fertilizer increased the relative abundance of copiotrophic bacteria and decreased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the soil of red raspberry orchard could indicate an increase in soil nutrient availability, which have positive implications for soil fertility and production. However, nitrogen fertilizer reduction with bio-organic fertilizer altered the abundance and diversity of soil bacteria, which was reduced compared to CF treatments. The PCoA analysis of the soil bacterial community showed that the community structure of NF-25% treatment was more different from other treatments, indicating that the fertilization method changed the community structure of soil bacteria. The results of a redundancy analysis showed that SOM, pH, AN, TN, and AP were the main factors affecting the microbial community structure. Overall, the reduction of nitrogen fertilizer with bio-organic fertilizer significantly increased the soil nutrient content, reduced the relative abundance and diversity of soil bacteria, increased the relative abundance of beneficial bacteria in the soil, changed the bacterial community structure of soil, increased production and created suitable soil conditions for the red raspberry growth.

Insight into the soil aggregate-mediated restoration mechanism of degraded black soil via biochar addition: Emphasizing the driving role of core microbial communities and nutrient cycling

Soil microbial communities are responsive to biochar application. However, few studies have investigated the synergistic effects of biochar application in the restoration of degraded black soil, especially soil aggregate-mediated microbial community changes that improve soil quality. From the perspective of soil aggregates, this study explored the potential microbial driving mechanism of biochar (derived from soybean straw) addition in black soil restoration in Northeast China. The results showed that biochar significantly improved the soil organic carbon, cation exchange capacity and water content, which play crucial roles in aggregate stability. The addition of biochar also significantly increased the concentration of the bacterial community in mega-aggregates (ME; 0.25-2 mm) compared with micro-aggregates (MI; <0.25 mm). Microbial co-occurrence networks analysis showed that biochar enhanced microbial interactions in terms of the number of links and modularity, particularly in ME. 16 S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, gltS, aclB, and mcrA) and nitrogen (nifH and amoA) transformation increased after the addition of biochar. Furthermore, the functional microbes involved in carbon fixation (Firmicutes and Bacteroidetes) and nitrification (Proteobacteria) were significantly enriched and are the key regulators of carbon and nitrogen kinetics. Structural equation model (SEM) analysis further showed that the application of biochar promoted soil aggregates to positively regulate the abundance of soil nutrient conversion-related microorganisms, thereby increasing soil nutrient content and enzyme activities. These results provide new insights into the mechanisms of soil restoration through biochar addition.

Application potential of Vaccinium ashei R. for cadmium migration retention in the mining area soil

Despite numerous reports on phytoremediation of heavy metals contaminated soil, there are few reports on plant retention of heavy metals in the mining area slope. This study was the first of its kind to explore the cadmium (Cd) retention capacity of the blueberry (Vaccinium ashei Reade). Firstly, we investigated the stress response of blueberry to different soil Cd concentrations (1, 5, 10, 15, 20 mg/kg) to assess its potential for phytoremediation by pot experiments. The results showed that the blueberry biomass exposed to 10 and 15 mg/kg Cd was significantly increased compared with the control (1 mg/kg Cd); the blueberry crown increased by 0.40% and 0.34% in 10 and 15 mg/kg Cd-contaminated soil, respectively, compared with control; the blueberry heigh did not even change significantly in each treatment group; the total chlorophyll content, peroxidase and catalase activity of blueberry were enhanced in 5-20 mg/kg Cd treatments. Furthermore, the Cd contents of blueberry in the root, stem and leaf increased significantly as the Cd concentration of soil increased. We found that more Cd accumulated in blueberry root: the bioaccumulation concentration factor was root > stem > leaf for all groups; the residual-Cd (Cd speciation) in soil increased by 3.83%-411.11% in blueberry-planted versus unplanted groups; blueberry improved the Cd-contaminated soil micro-ecological environment including soil organic matter, available K and P, as well as microbial communities. Then, to investigate the effect of blueberry cultivation on Cd migration, we developed a bioretention model and revealed that soil Cd transport along the model slope was significantly weakened by blueberry cultivation, especially at the bottom of the model. In a word, this research suggests a promising method for the phytoremediation of Cd-contaminated soil and the reduction of Cd migration in mining areas.

Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source

Members of the genus Pseudomonas have been frequently isolated from the marine environment, indicating their ecological role in native habitats. One bacterial strain, Pseudomonas sp. BSw22131, was isolated from seawater in Kongsfjorden, Svalbard. The bacterium can grow with algae-derived dimethylsulfoniopropionate (DMSP) as the sole carbon source. Here, we sequenced the complete genome of strain BSw22131, which contained a single circular chromosome of 5,739,290 (G + C content of 58.23 mol%) without any plasmids. A total of 5362 protein-coding genes, 65 tRNA genes, and 16 rRNA genes were obtained. Genome sequence analysis revealed that strain BSw22131 was not only a potential novel species of the genus Pseudomonas but also different from Pseudomonas sp. DMSP-1 that was isolated from the same habitat and also utilized DMSP as the sole carbon source for growth. The results can be helpful for understanding the catabolism of the genus Pseudomonas in sulfur cycling in the Arctic fjord ecosystem.

Effects of a Microbial Restoration Substrate on Plant Growth and Rhizosphere Microbial Community in a Continuous Cropping Poplar

In poplar cultivation, continuous cropping obstacles affect wood yield and soil-borne diseases, primarily due to structural changes in microbes and fungus infection. The bacterium Bacillus cereus BJS-1-3 has strong antagonistic properties against pathogens that were isolated from the rhizosphere soil of poplars. Poplar rhizospheres were investigated for the effects of Bacillus cereus BJS-1-3 on microbial communities. Three successive generations of soil were used to replant poplar seedlings. BJS-1-3 inoculated poplars were larger, had higher plant height and breast height diameter, and had a greater number of total and culturable bacteria than non-inoculated controls. B. cereus BJS-1-3 inoculated poplar rhizospheres were sequenced, utilizing the Illumina MiSeq platform to analyze changes in diversity and structure. The fungi abundance and diversity in the BJS-1-3 rhizosphere were significantly lower than in the control rhizosphere. In comparison to the control group, Bacillus sp. constituted 2.87% and 2.38% of the total bacterial community, while Rhizoctonia sp. constituted 2.06% and 6.00% of the total fungal community. Among the potential benefits of B. cereus BJS-1-3 in poplar cultivation is that it enhances rhizosphere microbial community structure and facilitates the growth of trees.

Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet

Microorganisms play critical ecological roles in the global biogeochemical cycles. However, extensive information on the microbial communities in Qinghai-Tibet Plateau (QTP), which is the highest plateau in the world, is still lacking, particularly in high elevation locations above 4500 m. Here, we performed a survey of th e soil and water microbial communities in Bamucuo Lake, Tibet, by using shotgun metagenomic methods. In the soil and water samples, we reconstructed 75 almost complete metagenomic assembly genomes, and 74 of the metagenomic assembly genomes from the water sample represented novel species. Proteobacteria and Actinobacteria were found to be the dominant bacterial phyla, while Euryarchaeota was the dominant archaeal phylum. The largest virus, Pandoravirus salinus, was found in the soil microbial community. We concluded that the microorganisms in Bamucuo Lake are most likely to fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway. This study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-elevation locations with 4555 m, confirming that QTP is a vast and valuable resource pool, in which many microorganisms can be used to develop new bioactive substances and new antibiotics to which pathogenic microorganisms have not yet developed resistance.

Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake

Introduction

As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities.

Methods

The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication.

Results

Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO₄ ^2- and HS^- might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways.

Discussion

Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.

Response of soil bacterial community to alpine wetland degradation in arid Central Asia

A large number of studies have reported the importance of bacterial communities in ecosystems and their responses to soil degradation, but the response mechanism in arid alpine wetlands is still unclear. Here, the non-degraded (ND), slightly degraded (SD), and heavily degraded (HD) regions of Bayinbuluk alpine wetland were used to analyzed the diversity, structure and function of bacterial communities in three degraded wetlands using 16S rRNA. The results showed that with the increase of degradation degree, the content of soil moisture (SM) and available nitrogen (AN) decreased significantly, plant species richness and total vegetation coverage decreased significantly, Cyperaceae (Cy) coverage decreased significantly, and Gramineae (Gr) coverage increased significantly. Degradation did not significantly affect the diversity of the bacterial community, but changed the relative abundance of the community structure. Degradation significantly increased the relative abundance of Actinobacteria (ND: 3.95%; SD: 7.27%; HD: 23.97%) and Gemmatimonadetes (ND: 0.39%; SD: 2.17%; HD: 10.78%), while significantly reducing the relative abundance of Chloroflexi (ND: 13.92%; SD: 8.68%; HD: 3.55%) and Nitrospirae (ND: 6.18%; SD: 0.45%; HD: 2.32%). Degradation significantly reduced some of the potential functions in the bacterial community associated with the carbon (C), nitrogen (N) and sulfur (S) cycles, such as hydrocarbon degradation (ND: 25.00%; SD: 1.74%; HD: 6.59%), such as aerobic ammonia oxidation (ND: 5.96%; SD: 22.82%; HD: 4.55%), and dark sulfide oxidation (ND: 32.68%; SD: 0.37%; HD: 0.28%). Distance-based redundancy analysis (db-RDA) results showed that the bacteria community was significantly related to the TC (total carbon) and Gr (P < 0.05). The results of linear discriminant analysis effect size (LEfSe) analysis indicate significant enrichments of Alphaproteobacteria and Sphingomonas in the HD area. The vegetation communities and soil nutrients changed significantly with increasing soil degradation levels, and Sphingomonas could be used as potential biomarker of degraded alpine wetlands.

Characterization of a novel micro-pressure double-cycle reactor for low temperature municipal wastewater treatment

To solve the deterioration of effluent caused by low temperature in urban sewage treatment plant in cold areas, a new type of reactor was proposed, the biochemical environmental and low-temperature operating characteristics of the reactor were studied. Through analysis of flow simulation and dissolved oxygen (DO) distribution when the aeration rate was 0.6 m³/h, it showed that there were many different DO environments in the reactor at the same time, which provided favourable conditions for various biochemical reactions. The operation test showed that the average effluent removal rate of COD, TN, NH₄⁺-N and TP was 92.53%, 74.57%, 89.61% and 96.04%, respectively. And there were a variety of functional bacteria related to nitrogen and phosphorus removal in the system, most of them with strong adaptability at low temperatures. Among the dominant microorganisms, Flavobacterium and Rhodobacter were related to denitrification, Aeromonas and Thiothrix were related to phosphorous removal. Denitrifying phosphorus removal was the main way of phosphorus removal. Picrust2 results showed that the reactor operated well at low temperature, and the regional difference distribution of nitrification genes further confirmed the existence of functional zones in the reactor. The results showed that the Micro-pressure Double-cycle reactor worked well at low temperature, which provided a new idea and way for the upgrading of urban sewage treatment plants in cold areas.

Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan

Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.

Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism

Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.

Irrigation water salinity structures the bacterial communities of date palm (Phoenix dactylifera)-associated bulk soil

The irrigation of date palms (Phoenix dactylifera) with saline groundwater is routinely practiced in the agroecosystems of arid environments because of freshwater scarcity. This leads to salts deposition in topsoil layers and increases soil salinization. However, how different irrigation sources affect soil microbiota is poorly understood. Bulk soil samples were collected from date farms receiving non-saline water and saline groundwater to examine bacterial communities using metabarcoding. Overall, bacterial diversity measures (Shannon diversity index, richness, and evenness) did not vary between irrigation sources. Bacterial communities were structured based on irrigation water sources and were significantly associated with their electrical conductivity. Of 5,155 operational taxonomic units (OTUs), 21.3% were unique to soil irrigated with saline groundwater, 31.5% received non-saline water irrigation, and 47.2% were shared. The Proteobacteria abundance was higher in soil under saline groundwater irrigation while Actinobacteriota abundance was lower. A compositional shift at the genera level was also evident; the abundance of Subgroup_10 and Mycobacterium was higher under saline groundwater irrigation. Mycobacterium was a key indicator of OTU under saline groundwater irrigation while Solirubrobacter was an indicator of non-saline water irrigation. Functional gene analyses showed enrichment of fatty acid, cell wall, and starch biosynthesis pathways in soil under saline groundwater irrigation. These findings provide insights into how "salinity filtering" influences bacterial communities, key taxa, and the potential metabolic function in soil under increasing irrigation water salinities, and have broad implications for arid agroecosystems.

Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa

Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.

Compositional Shifts in Microbial Diversity under Traditional Banana Cropping Systems of Sub-Saharan Africa

Simple Summary

In soil, the connection between microbial diversity and plant health is vital in terms of achieving the food security. Here, we suggested the study on soil microbial diversity in diverse cropping systems of banana adopted and followed by small holder farmers over the years. We tracked down the bacterial and fungal diversity in mono cropping and intercropping systems using advanced molecular techniques. Our outcomes likewise uncovered that the impact of cropping systems on bacterial and fungal increments in plant roots and rhizosphere soil. Hence, safeguarding of soil microbial diversity is profoundly significant taking into consideration of the contributions for plant buildups and rhizodeposits into the soil.

Abstract

Improvements in the crop productivity, soil health, and sustainable intensification should be premised on the better understanding of interactions between the cropping systems and soil microbial diversity. In this study, we assessed variations in the microbial communities across the traditional banana-based cropping systems of contrasting monocrop vigor (vigorous or V vs. non-vigorous or NV) and the cropping system (monocrop or MC vs. intercropped or IC) using 16S rDNA (V3–V4) and ITS2 amplicon deep sequencing via Illumina platform. Sequencing results of the bacterial and fungal communities showed high variability among MC and V cropping systems. The abundances of Proteobacteria, Firmicutes, and Actinobacteria were significantly higher in NV (non-vigorous) and V (vigorous) cropping systems; and the abundances of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes in the MC (monocropping) than IC (intercropping). There were high relative abundances of Pseudomonas (6.1–37.43%), Bacillus (4.5–20.4%), Rhizobium (1.4–6.5%), and Devosia (1.5–6.7%) in the cropping systems. The dominant family of fungal class Incertae_sedis was Mortierellales, which accounted for 8.79–41.12% of total taxa. This result indicated that the cropping systems are vital for supporting the dynamic microbial diversity specifically beneficial for bacterial communities that helps in promoting synergistic plant-soil interactions and total productivity under resource poor conditions of smallholder farmers in sub-Saharan Africa (SSA).

Biofertilizers can enhance nitrogen use efficiency of sugarcane

Fertilizers are costly inputs into crop systems. To compensate for inefficiencies and losses from soil, farmers apply on average double the amount of nitrogen (N) fertilizer acquired by crops. We explored if N efficiency improves with biofertilizers formulated with organic waste, mineral N or plant growth-promoting rhizobacteria (PGPR). We compared treatments receiving mineral N fertilizer or biofertilizers at industry-recommended (100%) or lower (60%) N rates at two commercial sugarcane farms. Biofertilizer at the 60% N-rate generated promising results at one farm with significantly higher biomass and sugar yield than the no-N control, which matched the 100% mineral N treatment. This yield difference was accompanied by a shift in microbial diversity and composition. Correlation analysis confirmed that shifts in microbial communities were strongly linked to soil mineral N levels, as well as crop productivity and yield. Microbial co-occurrence networks further revealed that biofertilizer, including treatments with an added PGPR, can enhance bacterial associations, especially in the context of complex fungal networks. Collectively, the results confirm that biofertilizers have quantifiable effects on soil microbial communities in a crop system setting, which underscores the opportunities for biofertilizers to promote N use efficiency and the circular N economy.

Succession of soil bacterial community along a 46-year choronsequence artificial revegetation in an arid oasis-desert ecotone

How the bacterial community structure and potential metabolic functions will change after revegetation in arid desert ecosystems is still unknown. We used high-throughput pyrosequencing to explore changes in soil bacterial diversity, structure and metabolic pathways, and the key driving factors along a chronosequence of 46-year Haloxylon ammodendron revegetation in an oasis-desert ecotone in the northwestern China. Our results indicated that establishment of H. ammodendron on shifting sand dunes significantly changed the structure of bacterial communities and increased their diversity and richness. The main dominant phyla were Actinobacteria (32.1-41.3%) and Proteobacteria (19.2-27.0%); in that, α-Proteobacteria (16.4-20.7%) were the most abundant Proteobacteria. Kocuria coexisted at different succession stage after year 0, and their relative abundance ranged from 3.8-9.0%. Principal coordinates analysis (PCoA) showed that bacterial community from the same revegetation site grouped together and generally separated from each other, indicating that significant shifts in bacterial community structure occurred after revegetation. LEfSe analysis identified unique biomarkers in the soil samples from seven sites. Moreover, PICRUSt analysis indicated similar overall patterns of metabolic pathways in different succession stage. Redundancy analysis (RDA) showed that total carbon, pH and total phosphorus were major abiotic factors driving the structure of bacterial communities, which explained 57.5% of the variation in bacterial communities. Our findings advance the current understanding of plant-soil interactions in the processes of ecological restoration and desertification reversal.

Insight into the mechanisms of ball-milled biochar addition on soil tetracycline degradation enhancement: Physicochemical properties and microbial community structure

A set of soil under the addition of ball-milled biochar (BM-biochar) from different feedstocks (wheat straw (WS) and rice husk (RH)) and pyrolysis temperature (300 °C, 500 °C, and 700 °C) was established to analyze the tetracycline (TC) degradation performance enhancement and greenhouse gas carbon dioxide (CO₂), and nitrous oxide (N₂O) emission reduction from various angles, including physicochemical properties of soil and microbial community structure. After 45 days' incubation, the pH value decreased slightly from 7.34 to 7.22 for WS biochar-treated soil, while slightly increased from 7.34 to 7.50 for RH biochar-treated soil. The lowest KCl-leachable TC concentrations of BMWS700 and RH700 was about 0.0037 mg/L. Ball-milled 500 °C and 700 °C biochars enhanced the removal rate of TC significantly. The maximum reduction of TC was from 2.17 to 0.079 mg/kg, equivalent to 96% removal after ball-milled 500 °C wheat straw biochar (BMWS500) addition, suggesting the promoting effect of biochars on microorganisms for adsorption and degradation of TC. Biochars' addition reduced CO₂ and N₂O emissions, BM-biochar enlarged this effect under the pyrolysis temperature 500 °C for both feedstock types. Ball milled rice husk biochar pyrolyzed under 500 °C (BMRH500) presented the maximum inhibitory effect CO₂ emission. The addition of BM-biochar changed the microbial community and diversity. The relative abundance of bacterium and fungus such as Proteobacteria, Acidobacteria, Chlorofexi, Mortierella, and Chaetomium increased due to BM-biochar addition, which promoted the degradation of TC and gave rise to more healthy soil environment for plant or microbes. The larger specific surface area, π-π interactions, hydrophobic interaction, and hydrogen bonding are account for better adsorption and degradation of TC by BM-biochars. This work elucidated the management of organic contaminants in real soil by BM-biochar.

Partial ozonation of returned sludge via high-concentration ozone to reduce excess sludge production: A pilot study

Partial ozonation of returned sludge via high and low concentration of ozone were compared to evaluate their efficiency in excess sludge production reduction. A pilot-scale system of anaerobic/anoxic/oxic (A/A/O) + ozonated sludge recycle (OSR) process was operated for 97 days, to investigate the effects of different ozone concentration (380 mg/L and 150 mg/L) on the nutrient removal capacity, sludge reduction rate, the excess sludge properties including settling, dewatering and anaerobic digestion (AD) performance. It was found that at the same total ozone dosage (13 mg/g MLSS, 25 mg/g MLVSS), the ozone of 380 mg/L achieved much higher organic matters and total excess sludge reduction (41.6% and 25.9%) than 150 mg/L applied (31.0% and 18.2%). It also laid less deterioration effect on the effluent quality and had better nutrient (COD, NH₄⁺-N, TN) removal capacity than 150 mg/L applied. Meanwhile, little difference was found in the settling, dewatering and AD properties of excess sludge from the two A/A/O + OSR processes. Meanwhile, sludge solubilization rate, BIOLOG ECO microplate, 16S rRNA sequencing were applied comprehensively to illustrate the reasons for above advantages of the elevated ozone dosage applied. It was clarified that compared to 150 mg/L, A/A/O + OSR with ozone of 380 mg/L had higher sludge solubilization rate, less impact on bacterial community distribution and utilization capacity of carbon sources in bioreactors.

Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

Effects of warming on the bacterial community and its function in a temperate steppe

As a significant environmental issue, global warming will have a significant impact on soil microorganisms, especially soil bacteria. However, the effects of warming on the network structure of bacterial communities and the function of ecosystems remain unclear. Therefore, we examined the effects of three-year simulated field warming on the complexity of soil bacterial communities and predicted functions in a temperate steppe of Inner Mongolia. Warming significantly increased the α-diversity of bacteria in 2018 but did not affect it in 2019 and 2020. Warming increased network complexity and stability and keystone taxa, and these bacterial taxa also associated more closely with each other, indicating that the protection of interactions between bacterial taxa is very important for the conservation of biodiversity. Warming significantly increased aerobic chemoheterotrophy, ureolysis, and chemoheterotrophy, suggesting that warming increased the ability of bacteria to decompose organic matter and the emission of greenhouse gases, such as CO₂ and CH₄. Collectively, warming will alter soil bacterial community structure and its potential functions, further affecting key functions in grassland belowground ecosystems.

High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling

Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria, Chloroflexi, Acidobacteria, and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m^-1). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.

A microbial consortium-based product promotes potato yield by recruiting rhizosphere bacteria involved in nitrogen and carbon metabolisms

The effect of a microbial consortium-based (MCB) biocontrol product, composed of Bacillus subtilis, Trichoderma harzianum strain and diatomaceous earth as a carrier, on potato yield, and potential modes of action for its effect were investigated. The MCB product (300 kg ha-1 ) was added to furrows in which the potato seed tubers each year for 3 years (2016, 2017 and 2018), while potato planting without the MCB product treatment served as the control. A metagenomic analysis indicated that bacterial phylotypes dominated the microbial community, with a relatively small contribution of archaea and fungal taxa. The relative abundance of beneficial bacterial taxa increased significantly in response to the MCB product treatment. Notably, a higher relative abundance of bacterial taxa with carbon fixation, carbon-degrading and nitrogen metabolism properties were observed in the MCB product-treated potato rhizosphere. This was also reflected in the identification of a greater abundance of genes encoding enzymes involved in nitrogen metabolism, carbon fixation and carbon degradation pathways in the conducted metagenomic analysis. The greater relative abundance of these beneficial bacterial taxa in the rhizosphere of MCB product-treated plots, as well as the higher abundance of genes associated with the indicated cellular processes, were associated with an increase in tuber yield. The observed changes in microbial community structure at an early stage of tuber development appears to have a beneficial impact on tuber yield.

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.

White Rann of Kachchh harbours distinct microbial diversity reflecting its unique biogeography

The understanding of sub-surface soil microbial diversity is limited at both saline and hypersaline ecosystems, even though salinity is found to affect the microbial community in aqueous and terrestrial environment. In this study, a phylo-taxonomy analysis as well as the functional characteristics of microbial community of flat salt basin of White Rann of Kachchh (WR), Gujarat, India was performed along the natural salinity gradient. The high throughput sequencing approach has revealed the numerical abundance of bacteria relative to the archaea. Salinity, TOC, EC and sulphate concentration might be the primary driver of the community distribution along the transect at WR. The much anticipated effect of salinity gradient on the microbial composition surprisingly turned out to be more speculative, with little variance in the community composition along the spatial distance of WR. The metabolic pathways involved in energy metabolism (like carbon, nitrogen, sulphur) along with environmental adaptive genes (like osmotic and oxidative stress response, heat and cold shock genes clusters) were abundantly annotated from shot-gun metagenomic study. The carbonic anhydrase harbouring bacteria Bacillus sp. DM4CA1 was isolated from WR, having a catalytic ability for converting the gaseous carbon dioxide in presence of calcium carbonate into calcite at 25 % higher rate as compared to non-harbouring strains. The enzyme has a role in multiple alternative pathways in microbial metabolism. With the array of results obtained, the study could become the new reference for understanding the diversity structure and functional characteristics of the microbial community of terrestrial saline environment.

The Responses to Long-Term Water Addition of Soil Bacterial, Archaeal, and Fungal Communities in A Desert Ecosystem

The response of microbial communities to continual and prolonged water exposure provides useful insight when facing global climate changes that cause increased and uneven precipitation and extreme rainfall events. In this study, we investigated an in situ manipulative experiment with four levels of water exposure (ambient precipitation +0%, +25%, +50%, and +100% of local annual mean precipitation) in a desert ecosystem of China. After 9 years of water addition, Illumina sequencing was used to analyze taxonomic compositions of the soil bacterial, archaeal, and fungal communities. The results showed significant increases in microbial biomass carbon (MBC) at higher amended precipitation levels, with the highest values reported at 100% precipitation. Furthermore, an increase in the bacterial species richness was observed along the water addition gradient. In addition, the relative abundance of several bacterial phyla, such as Proteobacteria, significantly increased, whereas that of some drought-tolerant taxa, including Actinobacteria, Firmicutes, and Bacteroidetes, decreased. In addition, the phyla Planctomycetes and Nitrospirae, associated with nitrification, positively responded to increased precipitation. Archaeal diversity significantly reduced under 100% treatment, with changes in the relative abundance of Thaumarchaeota and Euryarchaeota being the main contributors to shifts in the archaeal community. The fungal community composition was stable in response to water addition. Results from the Mantel test and structural equation models suggested that bacterial and archaeal communities reacted contrastingly to water addition. Bacterial community composition was directly affected by changing soil moisture and temperature, while archaeal community composition was indirectly affected by changing nitrogen availability. These findings highlight the importance of soil moisture and nitrogen in driving microbial responses to long-term precipitation changes in the desert ecosystem.

Effects of Different Continuous Cropping Years on Bacterial Community and Diversity of Cucumber Rhizosphere Soil in Solar-Greenhouse

The rhizosphere soils from 1, 3, 5, and 7 years of cucumber continuous cropping in solar-greenhouse were used as the research objects. The region of bacterial 16S rRNA was analyzed by Illumina MiSeq high-throughput sequencing technology. The effect of continuous cropping years on the microbial community structure and diversity in cucumber soil in the greenhouse was investigated. The physical and chemical properties of soil and the activities of urease and catalase were determined. The results showed that cucumber crop succession for different years affected the community composition of the bacteria at the phylum level, and the abundance of Proteobacteria, Chloroflexi, Gemmatimonadetes, Patescibacteria and Firmicutes gradually increased, while Actinobacteria in the soil significantly decreased. Among the top 15 significantly different genera, with the extension of successive years, the relative abundance of most genera in bacteria decreased after a small increase in year 3. The diversity results indicated that soil samples from continuous cropping for 7 years had the lowest community diversity. PICRUSt analysis showed a decreasing trend in soil bacterial function as the cucumber crop succession age increased. In environmental factor clustering analysis, the soil bacterial community was significantly correlated with pH, available nitrogen (AN), soil urease (SUR) and available phosphorus (AP), and the effect on the bacterial community was expressed as SUR > AP > AN > pH.

Metagenomic Insight Into Patterns and Mechanism of Nitrogen Cycle During Biocrust Succession

The successional ecology of nitrogen cycling in biocrusts and the linkages to ecosystem processes remains unclear. To explore this, four successional stages of natural biocrust with five batches of repeated sampling and three developmental stages of simulated biocrust were studied using relative and absolute quantified multi-omics methods. A consistent pattern across all biocrust was found where ammonium assimilation, mineralization, dissimilatory nitrite to ammonium (DNiRA), and assimilatory nitrate to ammonium were abundant, while denitrification medium, N-fixation, and ammonia oxidation were low. Mathematic analysis showed that the nitrogen cycle in natural biocrust was driven by dissolved organic N and NO₃^–. pH and SO₄^2– were the strongest variables affecting denitrification, while C:(N:P) was the strongest variable affecting N-fixation, DNiRA, nitrite oxidation, and dissimilatory nitrate to nitrite. Furthermore, N-fixation and DNiRA were closely related to elemental stoichiometry and redox balance, while assimilatory nitrite to ammonium (ANiRA) and mineralization were related to hydrological cycles. Together with the absolute quantification and network models, our results suggest that responsive ANiRA and mineralization decreased during biocrust succession; whereas central respiratory DNiRA, the final step of denitrification, and the complexity and interaction of the whole nitrogen cycle network increased. Therefore, our study stresses the changing environmental functions in the biocrust N-cycle, which are succession-dependent.

Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.

Protection from metal toxicity by Hsp40-like protein isolated from contaminated soil using functional metagenomic approach

Pollution in the environment due to accumulation of potentially toxic metals results in deterioration of soil and water quality, thus impacting health of all living organisms including microbes. In the present investigation, a functional metagenomics approach was adopted to mine functional genes involved in metal tolerance from potentially toxic metal contaminated site. Eukaryotic cDNA library (1.0-4.0 kb) was screened for the genes providing tolerance to cadmium (Cd) toxicity through a functional complementation assay using Cd-sensitive Saccharomyces cerevisiae mutant ycf1^Δ. Out of the 98 clones able to recover growth on Cd-supplemented selective medium, one clone designated as PLCc43 showed more tolerance to Cd along with some other clones. Sequence analysis revealed that cDNA PLCc43 encodes a 284 amino acid protein harbouring four characteristic zinc finger motif repeats (CXXCXGXG) and showing partial homology with heat shock protein (Hsp40) of Acanthamoeba castellanii. qPCR analysis revealed the induction of PLCc43 in the presence of Cd, which was further supported by accumulation of Cd in ycf1^Δ/PLCc43 mutant. Cu-sensitive (cup1^Δ), Zn-sensitive (zrc1^Δ) and Co-sensitive (cot1^Δ) yeast mutant strains were rescued from sensitivity when transformed with cDNA PLCc43 indicating its ability to confer tolerance to various potentially toxic metals. Oxidative stress tolerance potential of PLCc43 was also confirmed in the presence of H₂O₂. Present study results suggest that PLCc43 originating from a functional eukaryotic gene of soil community play an important role in detoxification of potentially toxic metals and may be used as biomarker in various contaminated sites.

PStrain: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data

MOTIVATION

The microbial community plays an essential role in human diseases and physiological activities. The functions of microbes can differ due to strain-level differences in the genome sequences. Shotgun metagenomic sequencing allows us to profile the strains in microbial communities practically. However, current methods are underdeveloped due to the highly similar sequences among strains. We observe that strains genotypes at the same single nucleotide variant (SNV) locus can be speculated by the genotype frequencies. Also, the variants in different loci covered by the same reads can provide evidence that they reside on the same strain.

RESULTS

These insights inspire us to design PStrain, an optimization method that utilizes genotype frequencies and the reads which cover multiple SNV loci to profile strains iteratively based on SNVs in a set of MetaPhlAn2 marker genes. Compared to the state-of-art methods, PStrain, on average, improved the performance of inferring strains abundances and genotypes by 87.75% and 59.45%, respectively. We have applied the PStrain package to the dataset with two cohorts of colorectal cancer (CRC) and found that the sequences of Bacteroides coprocola strains are significantly different between CRC and control samples, which is the first time to report the potential role of B. coprocola in the gut microbiota of CRC.

AVAILABILITY

https://github.com/wshuai294/PStrain.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.