Biochar alters the soil fauna functional traits and community diversity: A quantitative and cascading perspective.

With the widespread use of biochar, the cascading effects of biochar exposure on soil fauna urgently require deeper understanding. A meta-analysis quantified hierarchical changes in functional traits and community diversity of soil fauna under biochar exposure. Antioxidant enzymes (24.1 %) did not fully mitigate the impact of MDA (13.5 %), leading to excessive DNA damage in soil fauna (21.2 %). Concurrently, reproduction, growth, and survival rates decreased by 20.2 %, 8.5 %, and 21.2 %, respectively. Due to a 39.7 % increase in avoidance behavior of soil fauna towards biochar, species richness ultimately increased by 80.2 %. Compared to other feeding habits, biochar posed a greater threat to the survival of herbivores. Additionally, macrofauna were the most sensitive to biochar. The response of soil fauna also depended on the type, size, concentration, and duration of biochar exposure. It should be emphasized that as exposure concentration increased, the damage to soil fauna became more severe. Furthermore, the smaller the biochar sizes, the greater the damage to soil fauna. To mitigate the adverse effects on soil fauna, this study recommens applying biochar at appropriate times and selecting large sizes in low to medium concentrations. These findings confirm the threat of biochar to soil health from the perspective of soil fauna.

Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities.

BACKGROUND: Functional redundancy (FR) is widely present, but there is no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, and distinct assemblies of microorganisms in different communities playing the same functional roles are termed between-community FR. We proposed two formulas to respectively quantify the degree of functional redundancy within and between communities and analyzed the FR degrees of carbohydrate degradation functions in global environment samples using the genetic information of glycoside hydrolases (GHs) encoded by prokaryotes. RESULTS: Our results revealed that GHs are each encoded by multiple taxonomically distinct prokaryotes within a community, and the enzyme-encoding prokaryotes are further distinct between almost any community pairs. The within- and between-FR degrees are primarily affected by the alpha and beta community diversities, respectively, and are also affected by environmental factors (e.g., pH, temperature, and salinity). The FR degree of the prokaryotic community is determined by deterministic factors. CONCLUSIONS: We conclude that the functional redundancy of GHs is a stabilized community characteristic. This study helps to determine the FR formation process and influencing factors and provides new insights into the relationships between prokaryotic community biodiversity and ecosystem functions. Video Abstract.

Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review.

BACKGROUND: Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods of helminth parasite identification using microscopy are time-consuming and poor in terms of taxonomic resolution, and require skilled observers. DNA metabarcoding has emerged as a powerful alternative for assessing community composition in a variety of sample types over the last few decades. While metabarcoding approaches have been reviewed for use in other research areas, the use of metabarcoding for parasites has only recently become widespread. As such, there is a need to synthesize parasite metabarcoding methodology and highlight the considerations to be taken into account when developing a protocol. METHODS: We reviewed published literature that utilized DNA metabarcoding to identify gastrointestinal helminth parasites in vertebrate hosts. We extracted information from 62 peer-reviewed papers published between 2014 and 2023 and created a stepwise guide to the metabarcoding process. RESULTS: We found that studies in our review varied in technique and methodology, such as the sample type utilized, genetic marker regions targeted and bioinformatic databases used. The main limitations of metabarcoding are that parasite abundance data may not be reliably attained from sequence read numbers, metabarcoding data may not be representative of the species present in the host and the cost and bioinformatic expertise required to utilize this method may be prohibitive to some groups. CONCLUSIONS: Overall, using metabarcoding to assess gastrointestinal parasite communities is preferable to traditional methods, yielding higher taxonomic resolution, higher throughput and increased versatility due to its utility in any geographical location, with a variety of sample types, and with virtually any vertebrate host species. Additionally, metabarcoding has the potential for exciting new discoveries regarding host and parasite evolution.

A Comparative Analysis of Bacterial and Fungal Communities in Coastal and Inland Pecan Plantations.

Pecan forests (Carya illinoinensis) are significant contributors to both food and oil production, and thrive in diverse soil environments, including coastal regions. However, the interplay between soil microbes and pecan forest health in coastal environments remains understudied. Therefore, we investigated soil bacterial and fungal diversity in coastal (Dafeng, DF) and inland (Guomei, GM) pecan plantations using high-throughput sequencing. The results revealed a higher microbial diversity in the DF plantation than in the GM plantation, significantly influenced by pH and edaphic factors. The dominant bacterial phyla were Proteobacteria, Acidobacteriota and Bacteroidota in the DF plantation, and Acidobacteriota, Proteobacteria, and Verrucomicrobiota in the GM plantation. Bacillus, Nitrospira and UTCFX1 were significantly more abundant bacterial genera in DF soil, whereas Candidatus Udaeobacter, HSB_OF53-F07 and ADurbBin063-1 were more prevalent in GM soil. Basidiomycota dominated fungal sequences in the GM plantation, with a higher relative abundance of Ascomycota in the DF plantation. Significant differences in fungal genus composition were observed between plantations, with Scleroderma, Hebeloma, and Naucoria being more abundant in DF soil, and Clavulina, Russula, and Inocybe in GM soil. A functional analysis revealed greater carbohydrate metabolism potential in GM plantation bacteria and a higher ectomycorrhizal fungi abundance in DF soil. Significantly positive correlations were detected between certain bacterial and fungal genera and pH and total soluble salt content, suggesting their role in pecan adaptation to coastal environments and saline-alkali stress mitigation. These findings enhance our understanding of soil microbiomes in coastal pecan plantations, and are anticipated to foster ecologically sustainable agroforestry practices and contribute to coastal marshland ecosystem management.

Functional traits of exotic submerged macrophytes mediate diversity-invasibility relationship in freshwater communities under eutrophication.

Plant diversity may respond differently in terms of whether it can drive plant invasions in freshwater ecosystem. Linkages and interactions between diversity and invasibility have not been clearly resolved, and it is unclear how nutrient enrichment (e.g., eutrophication) will affect this relationship. As a key predictor of plant growth, the ability of functional traits to mediate trade-offs in the diversity-invasibility relationship is unknown. Here, we conducted a series of experiments to determine the role of exotic plant functional traits in the diversity-invasibility relationship of submerged macrophyte communities under eutrophication. We selected common native and exotic submerged macrophytes in the subtropics to construct different diverse submerged macrophyte communities to simulate invasion. Meanwhile, to test the adaptability and importance of functional traits, we experimentally verified the differences in functional traits between exotic and native species. Our results showed a positive correlation between native plant diversity and community invasibility. Moreover, the invader's performance was predominantly determined by functional traits of exotic species, such as plant biomass and tissue nutrients, which were significantly altered by species diversity. Furthermore, our results suggested that functional traits contribute significantly more to the invasiveness of exotic submerged macrophytes than the other factors to which they are subjected. Plant functional traits can mediate the diversity-invasibility relationship because of the higher intrinsic dominance of exotic submerged macrophyte species. In summary, our study revealed diversity-invasibility relationship in submerged macrophyte communities and highlighted functional traits as key drivers of invasion of high-risk exotic submerged macrophyte species. Although previous studies have elucidated the importance of functional trait studies for plant invasions, our study provides the only current evidence demonstrating the important role of invaders' functional traits in mediating the diversity-invasibility relationship. This novel perspective offers valuable insights into the management and control of invasive aquatic plants.

Seasonal variations in soil microbial community co-occurrence network complexity respond differently to field-simulated warming experiments in a northern subtropical forest.

Global warming may reshape seasonal changes in microbial community diversity and co-occurrence network patterns, with significant implications for terrestrial ecosystem function. We conducted a 2-year in situ field simulation of the effects of warming on the seasonal dynamics of soil microbial communities in a northern subtropical Quercus acutissima forest. Our study revealed that warming had no significant effect on the richness or diversity of soil bacteria or fungi in the growing season, whereas different warming gradients had different effects on their diversity in the nongrowing season. Warming also changed the microbial community structure, increasing the abundance of some thermophilic microbial species and decreasing the abundance of some symbiotrophic microorganisms. The co-occurrence network analysis of the microbial community showed that warming decreased the complexity of the intradomain network in the soil bacterial community in the growing and nongrowing seasons but increased it in the fungal community. Moreover, increasing warming temperatures increased the complexity of the interdomain network between bacteria and fungi in the growing season but decreased it in the nongrowing season, and the keystone species in the interdomain network changed with warming. Warming also reduced the proportion of positive microbial community interactions, indicating that warming reduced the mutualism, commensalism, and neutralism of microorganisms as they adapted to soil environmental stress. The factors affecting the fungal community varied considerably across warming gradients, with the bacterial community being significantly affected by soil temperature, MBC, NO3--N and NH4+-N, moreover, SOC and TN significantly affected fungal communities in the 4 °C warming treatment. These results suggest that warming increases seasonal differences in the diversity and complexity of soil microbial communities in the northern subtropical region, significantly influencing soil dynamic processes regulating forest ecosystems under global warming.

[Bacterial community diversity in human Demodex mites].

OBJECTIVE: To investigate the bacterial community diversity in human Demodex mites, so as to provide insights into unraveling the role of human Demodex mites in them caused infectious diseases. METHODS: From June to July 2023, Demodex mites were collected from the faces of college students in a university in Wuhu City using the adhesive tape method, and the V4 region of 16S ribosomal RNA (16S rRNA) gene and the internal transcribed spacer (ITS) gene of nuclear ribosomal DNA were amplified on an Illumina PE250 high-throughput sequencing platform. Sequencing data were spliced according to the overlapping relations and filtered to yield effective sequences, and operational taxonomic units (OTUs) was clustered. The diversity index of obtained OUTs was analyzed, and the structure of the bacterial community was analyzed at various taxonomic levels. RESULTS: A total of 57 483 valid sequences were obtained using 16S rRNA gene sequencing, and 159 OUTs were classified according to similarity. Then, OUTs at a 97% similarity were included for taxonomic analyses, and the bacteria in Demodex mites belonged to 14 phyla, 20 classes, 51 orders, 72 families, and 94 genera. Proteobacteria was the dominant phylum, and Vibrio, Bradyrhizobium and Variovorax were dominant genera. A total of 56 362 valid sequences were obtained using ITS gene sequencing, and 147 OTUs were obtained, which belonged to 5 phyla, 17 classes, 34 orders, 68 families, and 93 genera and were annotated to Ascomycota, Basidiomycota and Chytridiomycota, with Ascomycota as the dominant phylum, and Alternaria alternata, Epicoccum, Penicillium, and Sarocladium as dominant genera. CONCLUSIONS: There is a high diversity in the composition of bacterial communities in human Demodex mites, with multiple types of microorganisms and high species abundance.

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In this study, we explored the changes in plant community diversity and their relationship with soil factors under shrub encroachment pressure by selecting four marsh areas in Sanjiang Plain with different degrees of shrub cover (a, 0≤a≤100%), including marsh with no shrub encroachment (a=0), light shrub encroachment (0

Epiphytic Bacterial Community Analysis of Ulva prolifera in Garorim and Muan Bays, Republic of Korea.

The bacterial communities related to seaweed can vary considerably across different locations, and these variations influence the seaweed's nutrition, growth, and development. To study this further, we evaluated the bacteria found on the green marine seaweed Ulva prolifera from Garorim Bay and Muan Bay, two key locations on Republic of Korea's west coast. Our analysis found notable differences in the bacterial communities between the two locations. Garorim Bay hosted a more diverse bacterial population, with the highest number of ASVs (871) compared to Muan Bay's 156 ASVs. In Muan Bay, more than 50% of the bacterial community was dominated by Pseudomonadota. On the other hand, Garorim Bay had a more balanced distribution between Bacteroidota and Pseudomonadota (37% and 35.5%, respectively). Additionally, Cyanobacteria, particularly Cyanothece aeruginosa, were found in significant numbers in Garorim Bay, making up 8% of the community. Mineral analysis indicated that Garorim Bay had higher levels of S, Na, Mg, Ca, and Fe. Function-wise, both locations exhibited bacterial enrichment in amino acid production, nucleosides, and nucleotide pathways. In conclusion, this study broadens our understanding of the bacterial communities associated with Ulva prolifera in Korean waters and provides a foundation for future research on the relationships between U. prolifera and its bacteria.

Advancing two-stage hydrogen production from corn stover via dark fermentation: Contributions of thermally modified maifanite to microbial proliferation and pH self-regulation.

This study introduces a two-stage hydrogen production enhancement mechanism using natural particle additives, with a focus on the effects of thermally modified maifanite (TMM) and pH self-regulation on dark fermentation (DF). Initial single-factor experiments identified preliminary parameters for the addition of TMM, which were further optimized using a Box-Behnken design. The established optimal conditions which include mass of 5.5 g, particle size of 120 mesh, and temperature of 324 °C, resulted in a 28.7 % increase in cumulative hydrogen yield (CHY). During the primary hydrogen production stage, TMM significantly boosted the growth and activity of Clostridium_sensu_stricto_1, enhancing hydrogen output. Additionally, a pH self-regulating phenomenon was observed, capable of initiating secondary hydrogen production and further augmenting CHY. These findings presented a novel and efficient approach for optimizing biohydrogen production, offering significant implications for future research and application in sustainable energy technologies.

Screening of plant growth-promoting rhizobacteria helps alleviate the joint toxicity of PVC+Cd pollution in sorghum plants.

Combined microplastic and heavy metal pollution (CM-HP) has become a popular research topic due to the ability of these pollutants to have complex interactions. Plant growth-promoting rhizobacteria (PGPR) are widely used to alleviate stress from heavy metal pollution in plants. However, the effects and mechanisms by which these bacteria interact under CM-HP have not been extensively studied. In this study, we isolated and screened PGPR from CM-HP soils and analyzed the effects of these PGPR on sorghum growth and Cd accumulation under combined PVC+Cd pollution through pot experiments. The results showed that the length and biomass of sorghum plants grown in PVC+Cd contaminated soil were significantly lower than those grown in soils contaminated with Cd alone, revealing an enhancement in toxicity when the two contaminants were mixed. Seven isolated and screened PGPR strains effectively alleviated stress due to PVC+Cd contamination, which resulted in a significant enhancement in sorghum biomass. PGPR mitigated the decrease in soil available potassium, available phosphorus and alkali-hydrolyzable nitrogen content caused by combined PVC+Cd pollution and increased the contents of these soil nutrients. Soil treatment with combined PVC+Cd pollution and PGPR inoculation can affect rhizosphere bacterial communities and change the composition of dominant populations, such as Proteobacteria, Firmicutes, and Actinobacteria. PICRUSt2 functional profile prediction revealed that combined PVC+Cd pollution and PGPR inoculation affected nitrogen fixation, nitrification, denitrification, organic phosphorus mineralization, inorganic phosphorus solubilization and the composition and abundance of genes related the N and P cycles. The Mantel test showed that functional strain abundance, the diversity index and N and P cycling-related genes were affected by test strain inoculation and were significant factors affecting sorghum growth, Cd content and accumulation. This study revealed that soil inoculation with isolated and screened PGPR can affect the soil inorganic nutrient content and bacterial community composition, thereby alleviating the stress caused by CM-HP and providing a theoretical basis and data support for the remediation of CM-HP.

[Characteristics of Epiphytic Bacterial Community on Submerged Macrophytes in Water Environment Supplemented with Reclaimed Water].

Biofilms attached to submerged macrophytes play an important role in improving the water quality of the water environment supplemented with reclaimed water. In order to explore the effects of reclaimed water quality and submerged macrophyte species on the characteristics of an epiphytic bacterial community, different types of submerged macrophytes were selected as research objects in this study. 16S rRNA high-throughput sequencing technology was used on the epiphytic bacteria and the surrounding environmental samples to analyze the bacterial community structure and functional genes. The results showed that approximately 20%-35% of the nitrogen and phosphorus nutrients were absorbed and utilized in the water environment supplemented with reclaimed water. However, the COD, turbidity, and chroma of the downstream water were significantly increased. The bacterial community of the biofilms attached to submerged macrophytes was significantly different from that in the surrounding environment (soil, sediment, and water body) and in the activated sludge that was treated by reclaimed water. In terms of bacterial community diversity, the richness and diversity were significantly lower than those of soil and sediment but higher than those of plankton bacteria in water. In terms of bacterial community composition, dominant genera and corresponding abundances were also different from those of other samples. The main dominant bacterial genera were Sphingomonas, Aeromonas, Pseudomonas, and Acinetobacter, accounting for 7%-40%, respectively. Both macrophyte species and the quality of reclaimed water (BOD5, TN, NH4+-N, and TP) could affect the bacterial community. However, the effect of water quality of the bacterial community was greater than that of macrophytes species. Additionally, the quality of reclaimed water also affected the abundance of functional genes in the bacterial community, and the relative abundance of nitrogen and phosphorus cycling functional genes was higher in areas with higher nitrogen and phosphorus concentrations.

Parent material influences soil properties to shape bacterial community assembly processes, diversity, and enzyme-related functions.

Soil parent material is the second most influential factor in pedogenesis, influencing soil properties and microbial communities. Different assembly processes shape diverse functional microbial communities. The question remains unresolved regarding how these ecological assembly processes affect microbial communities and soil functionality within soils on different parent materials. We collected soil samples developed from typical parent materials, including basalt, granite, metamorphic rock, and marine sediments across soil profiles at depths of 0-20, 20-40, 40-80, and 80-100 cm, within rubber plantations on Hainan Island, China. We determined bacterial community characteristics, community assembly processes, and soil enzyme-related functions using 16S rRNA high-throughput sequencing and enzyme activity analyses. We found homogeneous selection, dispersal limitation, and drift processes were the dominant drivers of bacterial community assembly across soils on different parent materials. In soils on basalt, lower pH and higher moisture triggered a homogeneous selection-dominated assembly process, leading to a less diverse community but otherwise higher carbon and nitrogen cycling enzyme activities. As deterministic process decreased, bacterial community diversity increased with stochastic process. In soils on marine sediments, lower water, carbon, and nutrient content limited the dispersal of bacterial communities, resulting in higher community diversity and an increased capacity to utilize relative recalcitrant substrates by releasing more oxidases. The r-strategy Bacteroidetes and genera Sphingomonas, Bacillus, Vibrionimonas, Ochrobactrum positively correlated with enzyme-related function, whereas k-strategy Acidobacteria, Verrucomicrobia and genera Acidothermus, Burkholderia-Caballeronia-Paraburkholderia, HSB OF53-F07 showed negative correlations. Our study suggests that parent material could influence bacterial community assembly processes, diversity, and soil enzyme-related functions via soil properties.

Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer.

The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 µg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.

Effects of micro/nano-ozone bubble nutrient solutions on growth promotion and rhizosphere microbial community diversity in soilless cultivated lettuces.

Due to its high efficacy as a wide-spectrum disinfectant and its potential for the degradation of pollutants and pesticides, ozone has broad application prospects in agricultural production. In this study, micro/nano bubble technology was applied to achieve a saturation state of bubble nutrient solution, including micro-nano oxygen (O2 group) and micro-nano ozone (O3 group) bubble nutrient solutions. The effects of these solutions on lettuce physiological indices as well as changes in the microbial community within the rhizosphere substrate were studied. The application of micro/nano (O2 and O3) bubble nutrient solutions to substrate-cultured lettuce plants increased the amount of dissolved oxygen in the nutrient solution, increased the lettuce yield, and elevated the net photosynthetic rate, conductance of H2O and intercellular carbon dioxide concentration of lettuce plants. Diversity analysis of the rhizosphere microbial community revealed that both the abundance and diversity of bacterial and fungal communities in the substrate increased after plant cultivation and decreased following treatment with micro/nanobubble nutrient solutions. RDA results showed that the microbial community in the S group was positively associated with EC, that in the CK and O2 groups exhibited a positive correlation with SC, and that in the O3 group displayed a positive correlation with CAT and POD. Overall, the implementation of micro/nanobubble generation technology in soilless substrates can effectively increase the lettuce growth and yield, and O3 had a more pronounced effect on lettuce yield and quality and the microbial community structure in the substrate than O2. Our study would provide a reference and theoretical basis for developing sustainable and green technology for promoting lettuce production and can be a promising alternative to conventional methods for improving crop yields.

Diversity, Community Structure, and Antagonism of Endophytic Fungi from Asymptomatic and Symptomatic Mongolian Pine Trees.

Diplodia tip blight, caused by Diplodia sapinea (=Sphaeropsis sapinea), are widely distributed in Honghuaerji, Inner Mongolia, China, causing severe damage on natural Mongolian pine (Pinus sylvestris var. mongolica). D. sapinea is an endophyte that becomes pathogenic under conditions of drought, hail damage, or temperature-associated stress. The role of the endophytic community inhabiting different pine tissues in the expression of disease is still unknown. In this study, the diversity and community structure of endophytic fungi among asymptomatic and symptomatic Mongolian pine were detected using culture-based isolation and high-throughput sequencing (HTS), and the potential antagonistic endophytes against D. sapinea were also screened. The results indicated that 198 and 235 strains of endophytic fungi were isolated from different tissues of symptomatic and asymptomatic Mongolian pine, respectively. D. sapinea was the most common endophyte isolated from the current-year needles and shoots of symptomatic trees, and Diplodia was also the most common in the HTS data. There were no significant differences in the endophytic fungal species richness among asymptomatic and symptomatic trees, but there were differences observed within specific sampled tissues. The ANOSIM analysis confirmed that the endophytic fungi community structure significantly differed between sampling tissues among symptomatic and asymptomatic Mongolian pine. Furthermore, the antagonism study revealed Penicillium fructuariae-cellae with the ability to inhibit the growth of D. sapinea in vitro, and the potential performance of this fungus, acting as biological control agent, was evaluated under greenhouse. Our findings can pave the way to a better understanding of the interactions between D. sapinea, other endophytic fungi and their hosts, and provide helpful information for more efficient disease management strategies.

Microbiota associated with urban forests.

Urban forests are essential for maintaining urban ecological stability. As decomposers, soil microorganisms play an indispensable role in the stability of urban forest ecosystems, promoting the material cycle of the ecosystems. This study used high-throughput sequencing technology to explore the bacteria in six forest stands, including Phyllostachys edulis (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Meanwhile, the differences in fungal communities were investigated. The results show that ZL has the highest alpha diversity of bacterial communities, while its fungal community is the lowest; Proteobacteria is the most abundant bacterial phylum in the six forest stands; ZKQ has the highest fungal diversity. In addition, soil microbial communities are affected by environmental factors. Soil pH, organic matter (SOM), and available phosphorus (AP) significantly influence the compositions of urban forest soil microbial communities. This study revealed the differences in bulk soil (BS) microbial community structures among six forest stands and the relationship between environmental factors and soil microbial communities, which has important guiding significance for creating healthy and stable urban forests with profound ecological benefits.

Deciphering Differences in Microbial Community Diversity between Clubroot-Diseased and Healthy Soils.

Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.

Direct observations of microbial community succession on sinking marine particles.

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.

Soil microbial communities' contributions to soil ecosystem multifunctionality in the natural restoration of abandoned metal mines.

On a global scale, the restoration of metal mine ecosystem functions is urgently required, and soil microorganisms play an important role in this process. Conventional studies frequently focused on the relationship between individual functions and their drivers; however, ecosystem functions are multidimensional, and considering any given function in isolation ignores the trade-offs and interconnectedness between functions, which complicates obtaining a comprehensive understanding of ecosystem functions. To elucidate the relationships between soil microorganisms and the ecosystem multifunctionality (EMF) of metal mines, this study investigated natural restoration of metal mines, evaluated the EMF, and used high-throughput sequencing to explore the bacterial and fungal communities as well as their influence on EMF. Bacterial community diversity and composition were more sensitive to mine restoration than fungal community. Bacterial diversity exhibited redundancy in improving N-P-K-S multifunctionality; however, rare bacterial taxa including Dependentiae, Spirochaetes, and WPS-2 were important for metal multifunctionality. Although no clear relationship between fungal diversity and EMF was observed, the abundance of Glomeromycota had a significant effect on the three EMF categories (N-P-K-S, carbon, and metal multifunctionality). Previous studies confirmed a pronounced positive association between microbial diversity and multifunctionality; however, the relationship between microbial diversity and multifunctionality differs among functions' categories. In contrast, the presence of critical microbial taxa exerted stronger effects on mine multifunctionality.