Microbial Community Interactions Research Articles

Epiphytic and endophytic bacteria on Camellia oleifera phyllosphere: exploring region and cultivar effect

The epiphytic and endophytic bacteria play an important role in the healthy growth of plants. Both plant species and growth environmental influence the bacterial population diversity, yet it is inconclusive whether it is the former or the latter that has a greater impact. To explore the communities of the epiphytic and endophytic microbes in Camellia oleifera, this study assessed three representative C. oleifera cultivars from three areas in Hunan, China by Illumina high-throughput sequencing. The results showed that the diversity and species richness of endophytic microbial community in leaves were significantly higher than those of microbial community in the epiphytic. The diversity and species richness of epiphytic and endophytic microbes are complex when the same cultivar was grown in different areas. The C. oleifera cultivars grown in Youxian had the highest diversity of epiphytic microbial community, but the lowest abundance, while the cultivars grown in Changsha had the highest diversity and species richness of endophytic microbes in leaves. It was concluded that the dominant phylum mainly included Proteobacteria, Actinobacteriota and Firmicutes through the analysis of the epiphytic and endophytic microbial communities of C. oleifera. The species and relative abundances of epiphytic and endophytic microbial community were extremely different at the genus level. The analysis of NMDS map and PERMANOVA shows that the species richness and diversity of microbial communities in epiphytes are greatly influenced by region. However, the community structure of endophytic microorganisms in leaves is influenced by region and cultivated varieties, but the influence of cultivars is more significant. Molecular ecological network analysis showed that the symbiotic interaction of epiphytic microbial community was more complex.

Diel variations of airborne microbes and antibiotic resistance genes in Response to urban PM2.5 chemical properties during the heating season

Among the components of fine particulate matter (PM2.5), the contributions of airborne microorganisms and antibiotic resistance genes (ARGs) to health risks have been overlooked. Airborne microbial dynamics exhibit a unique diurnal cycle due to environmental influences. However, the specific roles of PM2.5 chemical properties resulting from fossil fuel combustion in driving circadian fluctuations in microbial populations and ARGs remain unclear. This study explored the interactions between toxic components and microbial communities during the heating period to understand the variations in ARGs. Bacterial and fungal communities showed a higher susceptibility to diel variations in PM2.5 compared to their chemical properties. Mantel tests revealed that chemical properties and microbial community interactions contribute differently to ARG variations, both directly and indirectly, during circadian fluctuations. Our findings highlight that, during the daytime, the enrichment of pathogenic microorganisms and ARGs increases the risk of PM2.5 toxicity. Conversely, during the nighttime, the utilization of water-soluble ions by the fungal community increased, leading to a significant increase in fungal biomass. Notably, Aspergillus exhibited a significant correlation with mobile genetic elements and ARGs, implying that this genus is a crucial driver of airborne ARGs. This study provides novel insights into the interplay between the chemical composition, microbial communities, and ARGs in PM, underscoring the urgent need for a comprehensive understanding of effective air pollution control strategies.

Insight into effect of polyethylene microplastic on nitrogen removal in moving bed biofilm reactor: Focusing on microbial community and species interactions

Microplastics (MPs) pollution has emerged as a global concern, and wastewater treatment plants (WWTPs) are one of the potential sources of MPs in the environment. However, the effect of polyethylene MPs (PE) on nitrogen (N) removal in moving bed biofilm reactor (MBBR) remains unclear. We hypothesized that PE would affect N removal in MBBR by influencing its microbial community. In this study, we investigated the impacts of different PE concentrations (100, 500, and 1000 μg/L) on N removal, enzyme activities, and microbial community in MBBR. Folin–phenol and anthrone colorimetric methods, oxidative stress and enzyme activity tests, and high-throughput sequencing combined with bioinformation analysis were used to decipher the potential mechanisms. The results demonstrated that 1000 μg/L PE had the greatest effect on NH4+-N and TN removal, with a decrease of 33.5 % and 35.2 %, and nitrifying and denitrifying enzyme activities were restrained by 29.5–39.6 % and 24.6–47.4 %. Polysaccharide and protein contents were enhanced by PE, except for 1000 μg/L PE, which decreased protein content by 65.4 mg/g VSS. The positive links of species interactions under 1000 μg/L PE exposure was 52.07 %, higher than under 500 μg/L (51.05 %) and 100 μg/L PE (50.35 %). Relative abundance of some metabolism pathways like carbohydrate metabolism and energy metabolism were restrained by 0.07–0.11 % and 0.27–0.4 %. Moreover, the total abundance of nitrification and denitrification genes both decreased under PE exposure. Overall, PE reduced N removal by affecting microbial community structure and species interactions, inhibiting some key metabolic pathways, and suppressing key enzyme activity and functional gene abundance. This paper provides new insights into assessing the risk of MPs to WWTPs, contributing to ensuring the health of aquatic ecosystems.

Biogeochemical traces and microbe-mineral interactions in the hyperarid core of the Atacama Desert

Life found various ways to thrive in hostile desert environments. Common adaptation mechanisms are protection against desiccation and UV radiation in biofilms and biocrusts as well as the hypolithic and endolithic colonization of rocks. One of those hostile regions is the Atacama Desert in Northern Chile with its hyperarid core, counted among the most arid places on Earth. Besides the aridity, life faces severe restrictions in this surrounding, e.g. extremely high UV radiation, scarce nutrient supply, and immense salt concentrations. Still, microbial communities and soil organic matter are crucial for the stability of soils and surface sediments in arid ecosystems. Combining molecular mass spectrometry for lipid biomarkers, scanning electron microscopy, and nuclear magnetic resonance spectroscopy, we individually investigated two factors that are of particular importance for the stability of dryland landscapes now and in the future: 1) We studied biogeochemical traces (organic remnants) in surface sediments along an aridity gradient with regard to possible decomposition and/or sequestration of organic compounds. 2) We investigated the interaction of lithobiontic and endolithic microbial communities with the mineral surface with special regard to the stability of soil and surface sediment structures in different areas of the Atacama Desert: in the region of the Salar Grande, Pisagua, and the Quebrada da Aroma. We analyzed halite- and calcium sulfate-dominated evaporitic crusts with and without visible microbial colonization. Organic traces were present in all investigated samples. Following an aridity gradient along the Quebrada de Aroma from an annual precipitation of about 20 mm to the hyperarid core with approx. 2 mm, we found a decrease in functionalized molecular compounds and plant-derived biomarkers (long-chain fatty acids, sterols) as well as an increase in aromatic hydrocarbons, indicating strongly decomposed remnants of plants and microorganisms. The investigation of halite- and calcium sulfate-dominated evaporitic crusts from the Salar Grande, Pisagua, and Aroma region revealed tight interactions of microorganisms with the mineral substrate. Indications of recent bacterial activity were ubiquitous (e.g. short-chain membrane fatty acids, carbohydrates of the extracellular polymeric substances (EPS)). Scanning electron microscopy revealed that especially the microbial EPS within evaporites seems to biochemically stabilize mineral aggregates by agglutination. Moreover, fungal biomarkers showed that fungi and fungal parts of lichen were not only present at the surface of physical soil crusts, but form widespread networks in the crusts and thereby contribute significantly to the physical stabilization of soils and surface sediments and to erosion protection.

Soil Bacterial Community of Medicinal Plant Rhizosphere in a Mediterranean System

Several attempts have been made to evaluate the abundance and distribution of the bacterial community in the rhizosphere of medicinal plants. Many describe information based on an estimation of the community structure and the effects of plant cover in determining microbial community composition. The ability of plants to specifically shape their microbial community in general and medicinal plants in particular is largely unknown. With the arrival of molecular biology, understanding the microbial community’s composition, diversity, and function became possible. We hypothesized that microbial communities associated with medicinal shrubs would differ from each other. To test this hypothesis, we characterized the soil microbial composition under each of five Mediterranean medicinal plants, differentiated by their medicinal use and ecophysiological adaptation, namely, Salvia fruticosa, Pistacia lentiscus, Myrtus communis, Origanum syriacum, and Teucrium capitatum, and an open-space bare soil between the plants, inhabiting natural ecosystems characterized by similar climatic conditions typical of a Mediterranean environment. The results demonstrated the importance of plant ecophysiological adaptations, which play an important role in determining microbial community composition and functional diversity. The intensity of a plant’s response to its surroundings can have either positive or negative effects that will determine the microbial community composition and interactions among the belowground parts. A total of 11 phyla, 21 orders, and 409 genera were found in the soil rhizosphere in the vicinity of the four plants and open space samples. The distinguishing attributes of each shrub trigger and stimulate the microbial community’s rhizosphere. This results in distinct patterns of bacterial diversity and functionality between the different shrubs and the control. The rhizosphere bacterial community composition differed between the plants in a PERMANOVA test, but there was little difference in terms of phyla and order relative abundances. This study shows how five medicinal plants, coexisting in a common habitat, impact the bacterial community. The noticeable shift in bacterial composition further supports our discovery that root exudates effectively govern the makeup of soil bacterial communities.

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates.

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

Unlocking the genome of the non-sourdough Kazachstania humilis MAW1: insights into inhibitory factors and phenotypic properties

BackgroundAscomycetous budding yeasts are ubiquitous environmental microorganisms important in food production and medicine. Due to recent intensive genomic research, the taxonomy of yeast is becoming more organized based on the identification of monophyletic taxa. This includes genera important to humans, such as Kazachstania. Until now, Kazachstania humilis (previously Candida humilis) was regarded as a sourdough-specific yeast. In addition, any antibacterial activity has not been associated with this species.ResultsPreviously, we isolated a yeast strain that impaired bio-hydrogen production in a dark fermentation bioreactor and inhibited the growth of Gram-positive and Gram-negative bacteria. Here, using next generation sequencing technologies, we sequenced the genome of this strain named K. humilis MAW1. This is the first genome of a K. humilis isolate not originating from a fermented food. We used novel phylogenetic approach employing the 18 S-ITS-D1-D2 region to show the placement of the K. humilis MAW1 among other members of the Kazachstania genus. This strain was examined by global phenotypic profiling, including carbon sources utilized and the influence of stress conditions on growth. Using the well-recognized bacterial model Escherichia coli AB1157, we show that K. humilis MAW1 cultivated in an acidic medium inhibits bacterial growth by the disturbance of cell division, manifested by filament formation. To gain a greater understanding of the inhibitory effect of K. humilis MAW1, we selected 23 yeast proteins with recognized toxic activity against bacteria and used them for Blast searches of the K. humilis MAW1 genome assembly. The resulting panel of genes present in the K. humilis MAW1 genome included those encoding the 1,3-β-glucan glycosidase and the 1,3-β-glucan synthesis inhibitor that might disturb the bacterial cell envelope structures.ConclusionsWe characterized a non-sourdough-derived strain of K. humilis, including its genome sequence and physiological aspects. The MAW1, together with other K. humilis strains, shows the new organization of the mating-type locus. The revealed here pH-dependent ability to inhibit bacterial growth has not been previously recognized in this species. Our study contributes to the building of genome sequence-based classification systems; better understanding of K.humilis as a cell factory in fermentation processes and exploring bacteria-yeast interactions in microbial communities.

Soil management shapes bacterial and archaeal communities in soybean rhizosphere: Comparison of no-tillage and integrated crop-livestock systems

Sustainable agricultural systems play a crucial role in improving soil properties and enhancing crop yields. Particularly for soybean, a vital agricultural commodity, no-tillage (NT) and integrated crop-livestock (ICL) systems have been employed in tropical regions. Despite the recognized benefits of using NT and ICL, there is a significant knowledge gap regarding their impact on the rhizosphere microbiome of soybean. Therefore, this field study aimed to explore and compare the responses of the bacterial and archaeal communities within the soybean rhizosphere in both NT and ICL systems. To address this objective, in addition to sampling the soybean rhizosphere, we collected samples from the bulk soil in the NT area and the rhizospheres of grass (Urochloa brizantha) and corn (Zea mays L.) in the ICL system, covering the typical land use in this region. The results revealed distinct bacterial and archaeal communities in the soybean rhizosphere under NT and ICL. Specifically, the ICL system enriched the soybean rhizosphere with KD4_96 (score 3), Vicinamibacteraceae (score 3), Candidatus Nitrocosmicus (score 2.5), and Methylobacterium (score 2.5). In contrast, NT led to an enrichment of Solirubrobacter (score 3), Amycolatopsis (score 2.8), Sphingomonas (score 2.8), and Nitrososphaeraceae (score 2.5). Microbial community interactions exhibited greater complexity in the soybean rhizosphere under NT (676 nodes and 7095 edges). Notably, both bacterial and archaeal communities in the soybean rhizosphere under NT and ICL demonstrated potential functionality in nitrogen fixation. Thus, this study showed that NT and ICL promoted different responses of bacterial and archaeal communities within the soybean rhizosphere which, can influence the plant's performance.

High synthetic cost-amino acids reduce member interactions of acetate-degrading methanogenic microbial community.

The cooperation among members of microbial communities based on the exchange of public goods such as 20 protein amino acids (AAs) has attracted widespread attention. However, little is known about how AAs availability affects interactions among members of complex microbial communities and the structure and function of a community. To investigate this question, trace amounts of AAs combinations with different synthetic costs (low-cost, medium-cost, high-cost, and all 20 AAs) were supplemented separately to acetate-degrading thermophilic methanogenic reactors, and the differences in microbial community structure and co-occurring networks of main members were compared to a control reactor without AA supplementation. The structure of the microbial community and the interaction of community members were influenced by AAs supplementation and the AAs with different synthetic costs had different impacts. The number of nodes, links, positive links, and the average degree of nodes in the co-occurrence network of the microbial communities with AAs supplementation was significantly lower than that of the control without AAs supplementation, especially for all 20 AAs supplementation followed by the medium- and high-cost AAs supplementation. The average proportion of positive interactions of microbial members in the systems supplemented with low-cost, medium-cost, high-cost, all AAs, and the control group were 0.42, 0.38, 0.15, 0.4, and 0.45, respectively. In addition, the ecological functions of community members possibly changed with the supplementation of different cost AAs. These findings highlight the effects of AAs availability on the interactions among members of complex microbial communities, as well as on community function.

The bioaugmentation effect of microbial inoculants on humic acid formation during co-composting of bagasse and cow manure

The effective degradation of recalcitrant lignocellulose has emerged as a bottleneck for the humification of compost, and strategies are required to improve the efficiency of bagasse composting. Bioaugmentation is a promising method for promoting compost maturation and improving the quality of final compost. In this study, the bioaugmentation effects of microbial inoculants on humic acid (HA) formation during lignocellulosic composting were explored. In the inoculated group, the maximum temperature was increased to 72.5 °C, and the phenol-protein condensation and Maillard humification pathways were enhanced, thus increasing the HA content by 43.85%. After inoculation, the intensity of the microbial community interactions increased, particularly for fungi (1.4-fold). Macrogenomic analysis revealed that inoculation enriched thermophilic bacteria and lignocellulose-degrading fungi and increased the activity of carbohydrate-active enzymes and related metabolic functions, which effectively disrupted the recalcitrant structure of lignocellulose to achieve a high humification degree. Spearman correlation analysis indicated that Stappia of the Proteobacteria phylum, Ilumatobacter of the Actinomycetes phylum, and eleven genera of Ascomycota were the main HA producers. This study provides new ideas for bagasse treatment and recycling and realizing the comprehensive use of resources.

Taxonomic and functional dynamics of nirS denitrifiers along a salinity gradient in the Pearl River Estuary

Understanding the factors that shape the diversity, distribution, and function of denitrifying microbes is vital for managing nitrogen cycling in these ecosystems. This study explores the diversity, biogeographic distribution, assembly processes, interaction, and denitrification potential of the nirS-encoding microbial community (nirS denitrifier) in the Pearl River Estuary based on high-throughput and metagenomics sequencing dataset. The results of this study show that salinity is a crucial regulatory environmental factor that determines the spatial distribution, phylogenetic turnover, and co-occurrence patterns of nirS denitrifiers. Additionally, the dissolved organic carbon (DOC), suspended sediment concentration (SSC), and dissolved oxygen (DO) in water also significantly impact the biodiversity and abundance of nirS denitrifiers. Furthermore, our findings demonstrate that, in comparison to environmental factors, the ecological and evolutionary characteristics of nirS denitrifiers play a more prominent role in regulating their denitrification potential, suggesting that alterations in the microbial community within dynamic changes in estuarine water can profoundly affect its denitrification function. Our results indicate the significant roles of denitrification microbial structure and phylogenetic characteristics in maintaining their ecological functions. Future studies should continue to explore the interactions between microbial communities and environmental factors to further elucidate the denitrification process in estuaries and its implications for ecosystem health and water quality.

Bacterial membrane vesicles: orchestrators of interkingdom interactions in microbial communities for environmental adaptation and pathogenic dynamics.

Bacterial membrane vesicles (MVs) have attracted increasing attention due to their significant roles in bacterial physiology and pathogenic processes. In this review, we provide an overview of the importance and current research status of MVs in regulating bacterial physiology and pathogenic processes, as well as their crucial roles in environmental adaptation and pathogenic infections. We describe the formation mechanism, composition, structure, and functions of MVs, and discuss the various roles of MVs in bacterial environmental adaptation and pathogenic infections. Additionally, we analyze the limitations and challenges of MV-related research and prospect the potential applications of MVs in environmental adaptation, pathogenic mechanisms, and novel therapeutic strategies. This review emphasizes the significance of understanding and studying MVs for the development of new insights into bacterial environmental adaptation and pathogenic processes. Overall, this review contributes to our understanding of the intricate interplay between bacteria and their environment and provides valuable insights for the development of novel therapeutic strategies targeting bacterial pathogenicity.

Exploring the Impact of Coconut Peat and Vermiculite on the Rhizosphere Microbiome of Pre-Basic Seed Potatoes under Soilless Cultivation Conditions.

Soilless cultivation of potatoes often utilizes organic coconut peat and inorganic vermiculite as growing substrates. The unique microbial communities and physicochemical characteristics inherent to each substrate significantly influence the microecological environment crucial for potato growth and breeding. This study analyzed environmental factors within each substrate and employed Illumina sequencing alongside bioinformatics tools to examine microbial community structures, their correlation with environmental factors, core microbial functions, and the dynamics of microbial networks across various samples. These included pure coconut peat (CP1) and pure vermiculite (V1), substrates mixed with organic fertilizer for three days (CP2 and V2), and three combinations cultivated with potatoes for 50 days (CP3, V3, and CV3-a 1:1 mix of coconut peat and vermiculite with organic fertilizer). Vermiculite naturally hosts a more diverse microbial community. After mixing with fertilizer and composting for 3 days, and 50 days of potato cultivation, fungal diversity decreased in both substrates. Coconut peat maintains higher bacterial diversity and richness compared to vermiculite, harboring more beneficial bacteria and fungi, resulting in a more complex microbial network. However, vermiculite shows lower bacterial diversity and richness, with an accumulation of pathogenic microorganisms. Among the 11 environmental factors tested, water-soluble nitrogen (WSN), total nitrogen (TN), available potassium (AK), total organic carbon (TOC) and air-filled porosity (AFP) were significantly associated with microbial succession in the substrate.The nutritional type composition and interaction patterns of indigenous microorganisms differ between vermiculite and coconut peat. Adding abundant nutrients significantly affects the stability and interaction of the entire microbial community, even post-potato cultivation. When using vermiculite for soilless cultivation, precise control and adjustment of nutrient addition quantity and frequency are essential.

Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats.

Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.

Interaction patterns and keystone taxa of bacterial and eukaryotic communities during sulfamethoxazole mineralization in lake sediment

Sulfamethoxazole (SMX) is a common antibiotic pollutant in aquatic environments, which is highly persistent under various conditions and significantly contributes to the spread of antibiotic resistance. Biodegradation is the major pathway to eliminate antibiotics in the natural environment. The roles of bacteria and eukaryotes in the biodegradation of antibiotics have received considerable attention; however, their successions and co-occurrence patterns during the biodegradation of antibiotics remain unexplored. In this study, 13C-labled SMX was amended to sediment samples from Zhushan Bay (ZS), West Shore (WS), and Gonghu Bay (GH) in Taihu Lake to explore the interplay of bacterial and eukaryotic communities during a 30-day incubation period. The cumulative SMX mineralization on day 30 ranged from 5.2 % to 19.3 %, which was the highest in WS and the lowest in GH. The bacterial community showed larger within-group interactions than between-group interactions, and the positive interactions decreased during incubation. However, the eukaryotic community displayed larger between-group interactions than within-group interactions, and the positive interactions increased during incubation. The proportion of negative interactions between bacteria and eukaryotes increased during incubation. Fifty genera (including 46 bacterial and 4 eukaryotic genera) were identified as the keystone taxa due to their dominance in the co-occurrence network and tolerance to SMX. The cumulative relative abundance of these keystone taxa significantly increased during incubation and was consistent with the SMX mineralization rate. These taxa closely cooperated and played vital roles in co-occurrence networks and microbial community interactions, signifying their crucial role in SMX mineralization. These findings broadened our understanding of the complex interactions of microorganisms under SMX exposure and their potential functions during SMX mineralization, providing valuable insights for in situ bioremediation.

Macrophyte coverage drives microbial community structure and interactions in a shallow sub-tropical lake

Shallow lakes are typically dominated by macrophytes, which have important functional roles regulating trophic conditions and creating biological habitat. Macrophytes have been shown to strongly influence water chemistry and shape microbial communities in shallow lakes. In Florida, many large, shallow lakes are dominated by alien invasive, submersed macrophytes, such as hydrilla (Hydrilla verticillata [L.F.] Royle) and are intensively managed to reduce infestations and contain the spread of these alien invasive macrophytes. In this study, we investigated the effects of large (40 ha) herbicidal and mechanical control treatments on a large lake located in Central Florida that resulted in the reduction of Hydrilla and concomitant changes in water chemistry and microbial communities (both bacteria and protists [microbial eukaryotes]). We observed a considerable decrease in macrophyte coverage associated with plant control treatments as well as a temporal change in macrophyte coverage in Lake Tohopekaliga. We found that changes in macrophyte coverage, regardless of treatment type, significantly affected the water chemistry of the lake, resulting in a sharp increase of chlorophyll a concentration as well as an increase in turbidity with the decrease of macrophyte coverage. Moreover, the decline in macrophytes led to decreases in microbial community diversity with over-representation of phototrophic functional groups. Specifically, we observed an increase in cyanobacteria with the decrease in macrophyte coverage. Our study highlights the advantages and disadvantages of macrophyte control. Although there was an initial decrease in macrophyte coverage associated with the chemical and mechanical control of aquatic plants, after a few months, we found a considerable increase in coverage. In addition, the increase of cyanobacterial relative abundance demonstrates the possible consequences of aquatic plant control such as cyanobacterial blooms if there is a continued decline of macrophytes.

Responses of plant diversity and soil microorganism diversity to nitrogen addition in the desert steppe, China

Nitrogen (N) deposition is a significant aspect of global change and poses a threat to terrestrial biodiversity. The impact of plant-soil microbe relationships to N deposition has recently attracted considerable attention. Soil microorganisms have been proven to provide nutrients for specific plant growth, especially in nutrient-poor desert steppe ecosystems. However, the effects of N deposition on plant soil microbial community interactions in such ecosystems remain poorly understood. To investigate these effects, we conducted a 6-year N-addition field experiment in a Stipa breviflora Griseb. desert steppe in Inner Mongolia Autonomous Region, northern China. Four N treatment levels (N0, N30, N50, and N100, corresponding to 0, 30, 50, and 100 kg N/(hm2•a), respectively) were applied to simulate atmospheric N deposition. The results showed that N deposition did not significantly affect the aboveground biomass of desert steppe plants. N deposition did not significantly reduce the alfa-diversity of plant and microbial communities in desert steppe, and low and mediate N additions (30 and 50 kg N/(hm2•a)) had a promoting effect on them. The variation pattern of plant Shannon index was consistent with that of the soil bacterial Chao1 index. N deposition significantly affected the beta-diversity of plants and soil bacteria, but did not significantly affect fungal communities. In conclusion, N deposition led to co-evolution between desert steppe plants and soil bacterial communities, while fungal communities exhibited strong stability and did not undergo significant changes. These findings help clarify atmospheric N deposition effects on the ecological health and function of the desert steppe.

Afforestation-Induced Shifts in Soil Bacterial Diversity and Community Structure in the Saihanba Region.

Afforestation plays a pivotal role in ecosystem restoration, exemplified by the Saihanba Mechanized Forest Farm, the world's largest planted forest; however, the assembly mechanisms and interactions of soil microbial communities in such forests remain inadequately understood. This study aimed to elucidate the impact of different afforestation tree species, namely Larix gmelinii var. principis-rupprechtii, Picea asperata, and Pinus sylvestris var. mongolica, on soil bacterial diversity and community structure in comparison to grassland. Sixty soil samples were collected at a 20 cm depth, and high-throughput sequencing was employed to identify bacterial communities and assess their interactions with environmental factors. A total of 6528 operational taxonomic units (OTUs) were identified, with Solirubrobacter, Conexibacter, Bacillus, Massilia, Gaiella, Acidibacter, and Vicinamibacter being the dominant genera. Afforestation significantly impacted soil bacterial alpha diversity, with notable influence from key soil chemical properties, including available phosphorus (AP), cation exchange capacity (CEC), and the carbon-to-nitrogen ratio of soil organic matter (SOM-C/N). The Mantel test highlighted pH, the Normalized Difference Vegetation Index (NDVI), and spatial variable (dbMEM) as primary environmental factors influencing dominant bacterial genera. The bacterial community structure demonstrated deterministic homogeneous selection, wherein SOM-C/N emerged as a significant factor influencing the dissimilarity of soil bacterial communities. Furthermore, plantation soils exhibited a more complex network structure than grassland soil, highlighting the crucial role of bacterial communities in vegetation changes and providing valuable insights into their response to environmental factors during the reforestation process.

Ecological dependencies and the illusion of cooperation in microbial communities.

Ecological dependencies - where organisms rely on other organisms for survival - are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amino acids. Legume plants similarly rely on nitrogen-fixing rhizobia to convert atmospheric nitrogen to ammonia. In some cases, dependencies can arise via loss-of-function mutations that allow one partner to benefit from the actions of another. It is common in microbiology to label ecological dependencies between species as cooperation - making it necessary to invoke cooperation-specific frameworks to explain the phenomenon. However, in many cases, such traits are not (at least initially) cooperative, because they are not selected for because of the benefits they confer on a partner species. In contrast, dependencies in microbial communities may originate from fitness benefits gained from genomic-streamlining (i.e. Black Queen Dynamics). Here, we outline how the Black Queen Hypothesis predicts the formation of metabolic dependencies via loss-of-function mutations in microbial communities, without needing to invoke any cooperation-specific explanations. Furthermore we outline how the Black Queen Hypothesis can act as a blueprint for true cooperation as well as discuss key outstanding questions in the field. The nature of interactions in microbial communities can predict the ability of natural communities to withstand and recover from disturbances. Hence, it is vital to gain a deeper understanding of the factors driving these dynamic interactions over evolutionary time.

Bisphenol A affects microbial interactions and metabolic responses in sludge anaerobic digestion.

The widespread use of bisphenol A (BPA) has resulted in the emergence of new pollutants in various environments, particularly concentrated in sewage sludge. This study investigated the effects of BPA on sludge anaerobic digestion, focusing specifically on the interaction of microbial communities and their metabolic responses. While the influence of BPA on methane accumulation is not significant, BPA still enhanced the conversion of soluble COD, protein, and polysaccharides. BPA also positively influenced the hydrolysis-acidogenesis process, leading to 17% higher concentrations of volatile fatty acids (VFAs). Lower BPA levels (0.2-0.5mg/kg dw) led to decreased hydrolysis and acidogenesis gene abundance, indicating metabolic inhibition; conversely, higher concentrations (1-5mg/kg dw) increased gene abundance, signifying metabolic enhancement. Diverse methane metabolism was observed and exhibited alterations under BPA exposure. The presence of BPA impacted both the diversity and composition of microbial populations. Bacteroidetes, Proteobacteria, Firmicutes, and Chloroflexi dominated in BPA-treated groups and varied in abundance among different treatments. Changes of specific genera Sedimentibacter, Fervikobacterium, Blvii28, and Coprothermobacter in response to BPA, affecting hydrolysis and acetogenesis. Archaeal diversity declined while the hydrogenotrophic methanogen Methanospirillum thrived under BPA exposure. BPA exposure enabled microorganisms to form structured community interaction networks and boost their metabolic activities during anaerobic digestion. The study also observed the enrichment of BPA biodegradation pathways at high BPA concentrations, which could interact and overlap to ensure efficient BPA degradation. The study provides insights into the digestion performance and interactions of microbial communities to BPA stress and sheds light on the potential effect of BPA during anaerobic digestion.