Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species.

BACKGROUD: The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. RESULTS: The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40-80.91% and 83.98-86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. CONCLUSION: The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

Fungal community characteristics and driving factors in Bothriochloa ischaemum litter in a copper mining area.

Among influencing biotic and abiotic factors, microorganisms predominate litter decomposition, playing an important role in maintaining the ecosystem material cycle. Bothriochloa ischaemum was the dominant plant species in China's Eighteen River tailings dam, and it was selected as the research object. We explored the dynamic of fungal community characteristics in B. ischaemum litter during different decomposition stages and investigated relevant driving factors affecting associative dynamic changes. Results showed that Ascomycetes and Basidiomycetes were the dominant phyla during litter decomposition. At a class level, the relative abundance of Dothideomycetes gradually decreased as litter decomposition progressed while Sordariomycetes gradually increased, ultimately becoming the dominant class. The community structure of the fungal community was mainly affected by litter pH, total carbon (TC), and copper (Cu) content. The fungal community's network structure was the most complex compared to other decomposition stages after 200 days of litter decomposition. Additionally, the fungal community's modularity gradually increased, while the degree of functional differentiation also increased, strengthening fungal community stability during litter decomposition. This study clarifies fungal community structure during litter decomposition in this copper tailings area, and provides a scientific basis for further improving soil fertility and nutrient cycling in mining areas.

Effect of AM Fungi Inoculation on Litter Bacterial Community Characteristics under Heavy Metal Stress.

Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. In this study, litter from the dominant plant species (Imperata cylindrica) in a copper tailings mining area was selected as the experimental material. We conducted a greenhouse-based heavy metal stress experiment to investigate how AM fungi affect litter microbial community characteristics and key ecological factors. Results showed that AM fungi species, heavy metal treatments, and their combined interaction had significant impacts on litter pH. Additionally, enzyme activities in litter were significantly affected by interactions between AM fungi species and heavy metal contaminates. Ralstonia was significantly positively correlated to lead (Pb) content, indicating that Ralstonia had a certain tolerance to Pb pollution. Sucrase and urease activity were increased when plants were inoculated with Rhizophagus irregularis under Pb stress. Furthermore, Microbacterium, Brevundimonas, and Pseudonocardia all may play important roles in litter decomposition, while a certain tolerance was observed in Kushneria and Roseivivax to heavy metal pollution when plants were inoculated with Glomus mosseae. Results showed that AM fungi affected litter bacterial community structure and function by influencing plant litter properties. By exploring interactions between AM fungi and bacterial communities in plant litter under heavy metal stress, we will better understand associative processes that promote the cycling of soil organic matter and nutrients contaminated by non-ferrous metal tailings.

Bacterial community succession and influencing factors for Imperata cylindrica litter decomposition in a copper tailings area of China.

Litter decomposition is a critical component of the ecological nutritional transformation process. In a copper mining area, the litter from Imperata cylindrica is the major indicator for restoring heavy metal-polluted copper mining lands. Large amounts of litter are generated at the end of the plant growing season during the process of vegetation restoration in copper mining areas, and the microbial dynamics play an important role in soil nutrient turnover during the decomposition of litter. Investigating the characteristics and interactions of bacterial communities during litter decomposition will clarify the driving mechanisms of organic matter and nutrient cycling in copper mining areas that harbor contaminated soils. Here, we report the results of an in situ decomposition experiment that lasted for a total of 460 days from three of the 16 copper mining subdams with heavy metal pollution and different phytoremediation histories (e.g., 50, 22 and 5 years) to explore the bacterial communities as the driving factors of litter decomposition. The total carbon contents of the litter decreased by 62.6% and 71.5% in the decomposition process at those sites with phytoremediation histories of 50 and 22 years (S516 and S536), respectively, but decreased by only 25.8% at the site with a phytoremediation history of 5 years (S560). The optimal C/N ratios in the three different restoration stages varied and were 65.5, 86.7 and 39.3 in S516, S536, S560, respectively. Litter decomposition enriched the heavy metal contents such as cadmium, copper (Cu), lead and zinc (P < 0.05) in litter. Proteobacteria and Actinobacteriota were the dominant bacterial phyla during the different litter decomposition stages, which accounted for 91.66% of the relative abundances in the bacterial communities. Moreover, the role of Friedmanniella, which had the highest betweenness centrality (BC) value, was critical in sustaining both the structure and function of the bacterial communities during the early decomposition stage. However, Quadrisphaera, with the maximum BC value (1074.8), became the dominant genus as litter decomposition progressed. The most crucial factors that affected the litter bacterial communities were the litter pH and copper contents. The obtained results will be helpful to provide a further understanding of litter decomposition mechanisms and will provide a scientific basis for improving the effectiveness of material circulation and nutrient transformation in degraded copper mining ecosystems.

Litter Decomposition of Imperata cylindrica in a Copper Tailing Areas With Different Restoration History: Fungal Community Dynamics and Driving Factors.

Microorganisms drive litter decomposition while maintaining the chemical cycle of ecosystems. We used the dominant vegetation (Imperata cylindrica) in the mining area selected for this study for this experiment to explore fungal community characteristics, key fungal groups, and their associative driving factors during I. cylindrica litter decomposition. Maximum litter C/N values occurred 100days after the commencement of the decomposition experiment during all different recovery years in this copper tailings area. Heavy metals in litter [copper (Cu), zinc (Zn), plumbum (Pb), and cadmium (Cd)] accumulated gradually with decomposition. The dominant fungal phyla observed in the community were Ascomycota and Basidiomycota, while the classes Sordariomycetes and Eurotiomycetes significantly increased as litter decomposition progressed. Degrees of connectivity and interaction between fungal communities were highest during the early litter decomposition stage. Sordariomycetes, Dothideomycetes, and Leotiomycetes all played critical roles in maintaining fungal community relationships. The effect of physicochemical properties and enzyme activities in I. cylindrica litter was significant on the dominant fungi, while driving factors that affected fungal communities differed over different recovery stages. Total nitrogen (TN), heavy metals, pH, and enzyme activities in the little were significantly correlated with fungal community composition. Litter properties throughout the litter decomposition process mainly affected the dynamics of the fungal community structure. The main environmental factors that affected fungal community structure were copper content and pH. Dichotomopilus, Trichoderma, Knufia, Phialophora, Oxyporus, and Monocillium, which all played important roles in litter decomposition, positively correlated with heavy metals, sucrase, and catalase. Finally, results from this study will help us better clarify litter decomposition mechanisms in degraded ecosystems as well as provide a scientific basis for improving species cycling and nutrient transformation efficiency in mining ecosystems.

Impact of Nutrients on Protozoa Community Diversity and Structure in Litter of Two Natural Grass Species in a Copper Tailings Dam, China.

In nature, protists directly participate in litter decomposition and indirectly affect litter decomposition processes by means of their influence on litter microbial communities. To date, relevant studies on litter microbial communities have primarily focused on bacteria and fungi, while relatively little attention has been paid to the characteristics of protozoan communities within damaged ecosystems. Two dominant grass species (Bothriochloa ischaemum and Imperata cylindrica) were selected from China's "Eighteenth" River tailings dam to explore protozoan community composition and diversity in a degraded mining area and to clarify the influence among key ecological factors and protozoan community characteristics in litter. High-throughput sequencing was used to analyze protozoan community composition and diversity, while correlation analysis was used to explore the relationships between protozoan communities and litter nutrient characteristics, including associative enzyme degradation. Although protozoan communities in litter shared a dominant group at an order level (Colpodida), they differed at a genus level (i.e., Hausmanniella and Tychosporium). Moreover, although the order Cryomonadida positively correlated to total nitrogen (TN) and sucrose, it exhibited an extreme negative correlation to total carbon (TC) and cellulase. Colpodida and Oomycota_X significantly and negatively correlated to litter urease activity. Nutrient characteristics of grass litter in copper tailing dams are important ecological factors that affect protozoan community characteristics. Notable differences were observed among protozoan communities of these two grass species, while litter enzyme activities were closely correlated to protozoan community diversity. The results suggested that Colpodida may play important roles in litter decomposition and nutrient cycling in mining areas.

Effects of Plant and Soil Characteristics on Phyllosphere and Rhizosphere Fungal Communities During Plant Development in a Copper Tailings Dam.

Interactions between plants and microbes can affect ecosystem functions, and many studies have demonstrated that plant properties influence mutualistic microorganisms. Here, high-throughput sequencing was used to investigate rhizosphere and phyllosphere fungal communities during different plant development stages. Results demonstrated that phyllosphere and rhizosphere fungal community structures were distinct during all developmental stages while they were mediated separately by plant carbon and soil sulfur. Comparatively, the effect of root properties on phyllosphere fungal diversity was greater than soil properties. Moreover, rhizosphere fungal networks of Bothriochloa ischaemum were more complex than phyllosphere fungal networks. This study demonstrated that the effect of plant and soil traits on phyllosphere and rhizosphere fungal communities could potentially be significant, depending on the applicable environmental condition and plant development stage. Although links between phyllosphere and rhizosphere communities have been established, further studies on functional fungal groups during phytoremediation processes are necessary. This study comprehensively analyzed dynamic relationships between phyllosphere and rhizosphere fungal communities during different plant development stages in a polluted environment. These fungal communities were determined to be expedient to the development and utilization of beneficial microbial communities during different development stages, which could more effectively help to stabilize and reclaim contaminated copper tailings soil.

Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam.

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

[Effects of Heavy Metal Contents on Phyllosphere and Rhizosphere Fungal Communities for Bothriochloa ischaemum in Copper Tailings Area].

There are complex interrelationships between plant microorganisms (phyllosphere and rhizosphere) and host plants, which can promote plant growth and enhance the tolerance of host plants to stress. In this study, we selected the dominant species Bothriochloa ischaemum as the research subject in a copper tailings dam. Using high-throughput sequencing, we investigated the structures of the fungal communities and diversities in the phyllosphere and rhizosphere of B. ischaemum. This study also explored the effects of heavy metal content on fungal community characteristics. The results showed that Ascomycota and Basidiomycota were the dominant phyla in the phyllosphere and rhizosphere of B. ischaemum. The diversities and richness of the rhizosphere fungal community were higher than that of the phyllosphere fungal community. The diversities of rhizosphere and phyllosphere fungal communities was affected by different heavy metals. Phyllosphere fungal diversity was mainly affected by the content of Zn and Cu in leaves, and the content of Pb in roots was the key factor affecting the diversity of the rhizophere fungal community. Furthermore, Pleosporaceae had a very significant positive correlation with Cd in the phyllosphere, and Nectriaceae had a significant positive correlation with Zn in the rhizosphere. These fungal communities could be used as indicators of ecological recovery in areas with heavy metal pollution. The results could provide an ecological basis for the exploration and utilization of phyllosphere or rhizosphere fungi resources during ecological restoration processes. This study also provides guidance for selecting the plant-microbial symbionts during ecological restoration in areas with heavy metal pollution.

Seasonal Microbial Community Characteristic and Its Driving Factors in a Copper Tailings Dam in the Chinese Loess Plateau.

A combined soil bacterial and fungal community survey was conducted for a copper tailings dam in the Chinese Loess Plateau. We investigated the seasonal differences in the composition and function of soil microbial community to examine the key environmental factors influencing soil microorganisms during restorative ecological processes. Significant seasonal differences were found in the community structure of both bacterial and fungal communities. Bacterial community abundance and fungal community (Shannon index) measurements were highest in summer. Soil nitrite nitrogen (NO2 --N) was the dominant factor influencing both bacterial and fungal communities. The bacterial community composition was significantly affected by NO2 --N and ammonium nitrogen (NH4 +-N) in spring, and fungal community structure was significantly affected by soil water content in autumn. Moreover, the fungal community exhibited significant functional feature differences among seasons, whereas bacterial community functional groups remained similar. This study aimed to clarify the adaptation response of microbes applying different approaches used in ecological restoration approaches specific to mining areas, and to identify the natural biofertility capacity of the microbial communities that colonize soil ecosystems.