Diversity Of Bacterial Communities Research Articles

Organic Amendments Enhance Peanut Nodulation by Influencing Interactions Between Rhizobia and Arbuscular Mycorrhizal Fungi in the Peanut Rhizosphere

The primary mechanism through which organic amendments enhance the nodulation ability of leguminous crops involves increasing the content of available phosphorus (AP) in the soil. Despite this, the role of plant rhizosphere microbial communities has not been fully appreciated. This study investigated the impact of different fertilization treatments, including a no-fertilizer control group (CK), a chemical nitrogen–phosphorus–potassium treatment group (NPK), and a group treated with both organic manure and chemical NPK (NPKM), on the structure of microbial communities in the peanut rhizosphere and their nodulation ability using high-throughput sequencing technology, co-occurrence network analysis, and structural equation modeling. The peanut nodule count increased significantly on organic manure plus NPK application, ranging from 2.26 to 2.50 times that of the CK treatment group. Under NPKM treatment, the diversity of bacterial and rhizobial communities in the peanut rhizosphere significantly improved. Co-occurrence network analysis showed that the peanut rhizosphere microbial co-occurrence network under NPKM treatment was more complex. Additionally, the ecological importance of rhizobial groups within the network significantly increased. Further analysis of the interaction patterns between different microbial groups revealed that under NPKM treatment, the positive correlation ratio between arbuscular mycorrhizal fungi (AMF) and rhizobia (RPAR) was significantly higher than that in the CK and NPK treatment groups. Structural equation modeling (SEM) analysis demonstrated that the RPAR significantly enhanced peanut nodulation ability, an effect that was positively modulated by AP. In summary, this study highlights the potential key role of the synergistic action between rhizobia and AMF in influencing the nodulation process of leguminous plants and provides a scientific basis for the effective management of plant microbial communities.

Dynamic Impact of One-Year Integrated Rice–Crayfish Farming on Bacterioplankton Communities in Paddy Water

As global food security issues become increasingly severe, an important innovation in agricultural production patterns, namely integrated rice–fish farming, has been widely implemented around the world, especially in Asia. To assess the impact of integrated rice–crayfish (Procambarus clarkii) farming (IRCF) on agricultural ecosystems, we used Illumina high-throughput 16S rRNA gene sequencing to analyze differences in diversity, composition, co-occurrence network, and assembly process of planktonic bacterial communities in paddy water between traditional rice farming (TRM) and IRCF. Environmental factors and planktonic bacterial communities were evaluated during the tillering, jointing, flowering, and grain-filling stages on August 24, September 5, September 24, and October 16, respectively. Our findings revealed that, throughout the entire cultivation period, IRCF had no notable impacts on bacterioplankton community diversity in paddy water, but it changed the composition and relative abundance of the dominant bacterioplankton. Specifically, IRCF promoted the Chloroflexota during the tillering stage but reduced its presence during the grain-filling stage. It also significantly decreased the Bacillota during the jointing stage while notably enhancing Actinomycetota during the flowering stage. Furthermore, IRCF markedly improved the robustness and negative/positive cohesion within bacterioplankton co-occurrence networks during jointing and grain-filling stages. IRCF altered the assembly processes shaping planktonic bacterial communities, promoting a greater dominance of stochastic processes during the tillering, jointing, and flowering stages and a diminished dominance during the grain-filling stage. IRCF dramatically changed aquatic environmental factors, particularly during the jointing stage, by substantially increasing the TN, ammonium, nitrate, and phosphate levels in paddy water. These nutrient levels were closely correlated with the dynamics of the planktonic bacterial communities. Our findings underscore the considerable potential of IRCF in enhancing the stability of bacterioplankton communities and promoting rice growth while also providing valuable data and theoretical insights into the microbiological ecological impacts of IRCF on the agroecosystem.

Hybrid Soybean as Green Manure for Improving Soil Properties and Subsequent Crop Growth

The rapid increase in fertilizer use has led to the degradation of soil quality, nutrient imbalances, reduced biodiversity, and soil compaction. To address these challenges, hybrid soybeans with efficient biological nitrogen fixation capabilities and broad environmental adaptability were selected as green manure to reduce fertilizer application, thereby improving soil fertility and structure. This study utilized the varieties “Forage Soybean S001” (S001), “Neinong S002 Forage Soybean” (S002), “Mengnong S003 Forage Soybean” (S003), “Mengnong S004 Forage Soybean” (S004), “Mengnong S005 Forage Soybean” (S005), and “Mengnong S006 Forage Soybean” (S006) as green manure materials. The clean tillage (CK) treatment served as the control, ensuring a residue-free soil surface while maintaining consistent practices in soil preparation, irrigation, and field management across all treatments. Field planting of green manure and subsequent crops was conducted at the M-Grass Ecology and Environment (Group) Company’s experimental site in Hohhot in early May of 2023 and 2024. The plots each measured 20 m2, with three replications arranged in a randomized block design. A combination of field experiments and laboratory analyses was utilized to investigate the effects of incorporating various hybrid soybean varieties as green manure on soil nutrient levels, soil enzyme activity, soil microbial communities, and the subsequent growth of oats. The results indicated that incorporating various hybrid soybean varieties as green manure into the soil significantly improved soil nutrient levels and enzyme activity. The diversity and richness of soil bacterial communities increased significantly, accompanied by alterations in community structure and composition. These changes enhanced soil fertility and optimized the microbial community structure, promoting the growth of subsequent crops. Among all the treatments, S001 and S004 were particularly effective in enhancing the soil environment, indicating their potential as superior green manure resources for broader application.

Difference in Community Structure and Function of Bacteria Attached to Stems and Leaves of Potamogeton crispus Compared to that of Bacteria in the Overlying Water and Sediment

The stems and leaves of submerged macrophytes usually grow below the water surface and could provide a good biological carrier for the colonization and growth of planktonic bacteria in water. Therefore, attached bacteria on the stem and leaf surfaces of submerged macrophytes are important components and play a crucial role in aquatic ecosystems. To further understand the structure characteristics and functional differences of the bacterial community attached to the stems and leaves of submerged macrophytes, the submerged macrophytes Potamogeton crispus and the overlying water and sediment were sampled and analyzed in this study. The results showed that a total of 10 320 OTUs were detected in the P. crispus samples, the overlying water samples, and the sediment samples. These OTUs included 64 phyla, 189 classes, 448 orders, 721 families, and 1 366 genera. The richness and diversity of bacterial communities in sediments were the highest, followed by the stem and leaves of P. crispus, and the alpha diversity index of planktonic bacteria in water was the lowest. Significant differences （P<0.05） were observed among the four alpha diversity indices of the three source samples. Bacterial communities with greater similarity were obtained from the same source samples, but there was more distinct community composition dissimilarity in bacteria collected from the submerged macrophytes and the overlying water and sediment samples （P<0.05）. At the level of phylum, order, and genus classification, the relative abundance of most dominant bacterial species, non-dominant species, and occasional species showed significant differences among the three source samples （P<0.05）. Proteobacteria, Actinobacteria, and Bacteroidetes were common dominant bacterial phyla for the three source samples, while Firmicutes were unique dominant phyla for attachment bacteria on the plant stem and leaves of P. crispus. There were differences in carbohydrate metabolism, energy metabolism, amino acid metabolism, cofactors, and vitamin metabolism among the three source samples （P<0.05）. The relative abundance of chemical heterotrophic and oxidative heterotrophic functional types in the stem and leaf samples of P. crispus was higher than that in the overlying water and sediment samples. In addition, higher nitrate reduction, nitrogen respiration, and nitric acid respiration functions were observed in sediment samples. To summarize, the stems and leaves have the potential to encourage bacterial colonization and create a unique bacterial community on the surface of submerged macrophytes. Submerged P. crispus macrophytes and their surroundings （water and sediment） play different roles in the biogeochemical cycling of nutrients in the freshwater ecosystem.

Effect of Nitrification Inhibitors on Soil Nitrogen Dynamics and Microbial Community Structure in Aerated Paddy Field

The aim of this study was to clarify the effects of nitrification inhibitors on the dynamic changes in the nitrogen and microbial community in paddy soil under aerated irrigation by using the indica hybrid rice Zhongzheyou 8 as experimental material. A trial with three treatments was conducted in 2023： conventional flooding irrigation （CF）, micro-nano bubble water aeration irrigation （MB）, and micro-nano bubble water aeration irrigation combined with nitrification inhibitor （MBNI）. The effects of nitrification inhibitors on the contents of NH4+-N and NO3--N and the apparent nitrification rate of soil under aerated irrigation were analyzed, as well as the characteristics of bacterial community diversity and its correlation with soil chemical factors. The results showed that compared with those in the CF treatment, the MB and MBNI treatment significantly increased the dissolved oxygen concentration, oxidation-reduction potential, pH, and soil NH4+-N content. Compared with that under the MB treatment, the MBNI treatment increased soil pH, reduced NH4+-N content in a short time after nitrogen fertilizer application, and later increased NO3--N content. Compared with that in the CF treatment, the MB and MBNI treatments could increase the diversity and richness of soil bacteria, while the relative abundance of Proteobacteria and Nitrospirota significantly increased, and the relative abundance of Bacteroidota decreased. The MBNI treatment reduced the diversity and richness of bacteria compared with that in the MB treatment and significantly decreased the relative abundance of Nitrospirota. Correlation analysis showed that soil chemical properties were significantly correlated with bacterial community structure. In conclusion, the combined application of nitrification inhibitors under aerated irrigation can improve soil nitrogen supply capacity, increase soil inorganic nitrogen content, improve soil chemical properties, and affect microbial community diversity and richness to optimize microbial community structure.

Effects of Different Fertilization Treatments on Bacterial Community and Citrus Quality in Yellow Soils of the Yunnan-Guizhou Plateau

To investigate the intrinsic driving mechanism of citrus yield and quality enhancement under different fertilizer applications, a field experiment was conducted to study the effects of biochar （SW）, organic fertilizer （YJ）, farmyard manure （NJ）, chemical fertilizer （HF）, and no fertilizer as the control （CK） on soil physical and chemical properties, bacterial community characteristics, and citrus quality of citrus orchards in the yellow soil area of the Yunnan-Guizhou Plateau. The results showed that compared with those in the CK treatment, the yield, single fruit weight, edible rate, juice rate, vitamin C content, and soluble solids of citrus increased under the different fertilization treatments. In contrast, the titratable acid content of citrus decreased, resulting in an increase in the solid-acid ratio of citrus. Among the different fertilization treatments, the most significant effective treatment was SW. The SW and YJ treatments significantly increased the soil pH value, while the HF treatment decreased soil pH. Different fertilization treatments could increase the contents of soil organic matter, hydrolyzable nitrogen, available phosphorus, and available potassium. The SW treatment exhibited the most obvious effect on the contents of soil hydrolyzable nitrogen, available phosphorus, and available potassium. The YJ treatment exhibited the most obvious effect on the soil organic matter content. The different fertilization treatments significantly affected soil bacterial community diversity and community structure, among which the SW treatment significantly increased the soil Chao1 index, observed species index, and Shannon index； optimized soil bacterial community structure； and made the bacterial symbiotic network simple and stable. By contrast, the HF treatment significantly decreased the soil Chao1 index, observed species index, and Simpson index and had less effect on bacterial community structure. Redundancy analysis showed that soil available potassium （96.47%）, Chao1 index （73.80%）, and Chujaibacter （55.92%） were the key factors in improving citrus yield and quality. Variance decomposition analysis indicated that the soil bacterial community structure was the largest contributor （17.00%） to the improvement in citrus yield and quality. In conclusion, fertilization can effectively improve soil physical and chemical properties, increase soil nutrient supply level, optimize bacterial community structure, and improve citrus yield and quality. Of these, biochar can be used as a priority for the fertilization and improvement of the soil in citrus orchards in the yellow soil area of the Yunnan-Guizhou Plateau.

Salt stress affects the bacterial communities in rhizosphere soil of rice

Salt is a primary factor limiting the utilization of saline lands in coastal beach areas, with rhizosphere microorganisms playing a crucial role in enhancing crop stress resistance and exhibiting high sensitivity to environmental changes. Rice (Oryza sativa L.) is the preferred crop for reclaiming salinized soils. This study determined the microbial communities in rhizosphere soil of rice under different salt stress treatments by high-throughput sequencing. We found that salt stress changed the bacterial community diversity, structure and function in rhizosphere soil of rice. Salt stress significantly reduced the richness and diversity of bacterial communities in rhizosphere soil of rice. The bacterial community was characterized by higher abundance of the phyla Chloroflexi, Proteobacteria and Actinobacteria; the relative abundances of Firmicutes, Acidobacteriota and Myxococcota were decreased, while Bacteroidota and Cyanobacteria were increased under salt stress. The functions of bacterial communities in rhizosphere soil of rice mainly include chemoheterotrophy, aerobic_chemoheterotrophy, phototrophy etc., chemoheterotrophy and aerobic_chemoheterotrophy were significantly higher NS3 (adding 3‰ NaCl solution to the base soil) treatment than NS6 (adding 6‰ NaCl solution to the base soil) treatment. These findings provide a theoretical foundation for the development of specialized salt-tolerant microbial agents for rice cultivation and offer a viable strategy for improving the soil environment of saline coastal lands through the application of beneficial microorganisms.

Impacts of phosphate-solubilizing bacterium strain MWP-1 on vegetation growth, soil characteristics, and microbial communities in the Muli coal mining area, China

Due to the cold climate and low soil nutrient content, high-altitude mining areas are challenging to restore ecologically. Their poor nutrient content may be ameliorated by introducing specific microorganisms into the soil. This study aims to evaluate the effects of a highly efficient phosphate solubilizing bacterium MWP-1, Pseudomonas poae, on plant growth, soil nutrients in remedying the soil of the high-altitude Muli mining area in Qinghai Province, and analyze its impact on microbial communities through high-throughput sequencing soil microbial communities. The results showed that MWP-1 significantly increased the content of soil available phosphorus by >50%, soil organic matter and total nitrogen by >10%, and significantly increased the height, coverage, and aboveground biomass of vegetation by >40% in comparison with the control (p < 0.05). MWP-1 mainly affected the composition of the soil bacterial communities at the taxonomic level below the phylum. Its impact on soil fungal communities occurred at the phylum and below taxonomic levels. In addition, MWP-1 also significantly improved the diversity of soil bacterial and fungal communities (p < 0.05), and changed their functions. It also significantly altered the relative abundance of genes regulating phosphorus absorption and transport, inorganic phosphorus dissolution and organic phosphorus mineralization in the bacterial community (p < 0.05). It caused a significant increase in the relative abundance of the genes regulating nitrogen fixation and nitrification in nitrogen cycling (p < 0.05), but a significant decrease in the genes regulating phospholipase (p < 0.05). Although sequencing results indicated that Pseudomonas poae did not become the dominant species, its dissolved phosphorus elements can promote plant growth and development, enrich soil nutrient content, and affect the succession of microbial communities, enhance ecosystem stability, with an overall positive effect on soil remediation in the mining area.

Grey and harbor seals in France (mainland and Saint-Pierre et Miquelon): microbial communities and identification of a microbial source tracking seal marker.

Seals, protected wild marine mammals, are widely found in waters around the world. However, rising concerns about their increasing numbers in some areas have led to potential worries regarding microbiological contamination of coastal areas by their feces, which could impact bathing and shellfish-harvesting activities. To the best of our knowledge, no study has been conducted on the bacterial and RNA viral communities present in the feces of both grey and harbor seals, which are the two main seal species observed in mainland France and overseas. Fecal bacterial (n = 132) and RNA viral (n = 40) communities of seals were analyzed using 16S rRNA gene amplicon high-throughput sequencing and viral RNA sequencing methods, respectively. In addition, to identify the specific characteristics of seal fecal microbial communities compared to other animal fecal microbial communities that may also contaminate coastal areas, the bacterial communities of seals were compared to those of wild waterbirds and breeding animals (i.e., cattle and pigs) which could be present in upstream catchments of coastal areas. Finally, ANCOM was used to identify unique and seal-associated Amplicon Sequence Variants (ASVs), aiming to develop a Microbial Source Tracking (MST) bacterial qPCR marker associated with seals. The bacterial communities of grey and harbor seals were not found to be significantly different and were characterized by a predominance of Firmicutes, including the genera Clostridium sensu stricto 1 and Peptoclostridium, followed by Fusobacteriota with the genus Fusobacterium, and Bacteroidota with the genus Bacteroides. However, variations in bacterial communities between sites and individuals were observed. Similar observations were made for the RNA viral communities being characterized by a predominance of Picobirnaviridae (44% of total reads) and Astroviridae (15%). This study successfully developed a sensitive (89.8%) and specific (97.1%) MST qPCR marker targeting grey seal-associated bacteria belonging to the Bifidobacteriaceae family. This marker can be used to identify potential fecal contamination of coastal areas by seals and complements the MST toolboxes of markers already developed for humans, wild birds and livestock.

The effect of Torreya grandis inter-cropping with Polygonatum sibiricum on soil microbial community.

Inter-cropping is a reasonable planting pattern between different plants. Inter-cropping of Torreya grandis with Polygonatum sibiricum is a relatively mature planting pattern in China, which has been applied to improve soil ecological environment and reduce the occurrence of pests and diseases in China. However, there is currently limited knowledge on the response of soil microbial communities to this practice. In this study, we employed Illumina MiSeq sequencing coupled with Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Fungi Functional Guild (FUNGuild) analyses to investigate the dynamic changes in soil microbial communities across seven treated groups [the bulk soil of the T. grandis inter-cropping with P. sibiricum (IB), the bulk soil for mono-cropping of P. sibiricum (PB), the bulk soil for mono-cropping of T. grandis (TB), the P. grandis rhizosphere soil of the T. grandis inter-cropping with P. sibiricum (IPR), the rhizosphere soil for mono-cropping of P. sibiricum (PR), the T. grandis rhizosphere soil of the T. grandis inter-cropping with P. sibiricum (ITR), and the rhizosphere soil for mono-cropping of T. grandis (TR)]. The results showed that the rhizosphere soil of Torreya-Polygonatum inter-cropping exhibited higher microbial community richness, diversity and evenness than mono-cropping (ITR > TR, IPR > PR). Inter-cropping increased the abundance of Micrococcaceae, Xanthobacteraceae, Saitozyma, while decreased Bacillus, Burkholderia, Streptomyces, Cladosporium, and Gibberella significantly of the rhizosphere soil of T. grandis. Further, the abundance of pathogens, such as Fusarium and Neocosmospora, was higher in mono-cropping samples compared to inter-cropping. There existed distinct variations in bacterial and fungal communities among all groups except for IB and TB. The FAPROTAX and FUNGuild analyses results indicated that inter-cropping significantly enhanced soil microbial function associated with nutrient cycling and exhibited a consistent increase in the relative abundance of nitrogen-cycling and carbon-cycling bacteria, and decreased the abundance of plant pathogen guild in the inter-cropping sample ITR compared to the mono-cropping TR. Our findings suggest that T. grandis inter-cropping with P. sibiricum not only enhance the diversity of soil microbial communities, but also improve the nitrogen and carbon cycling functions. In addition, the inter-cropping can effectively reduce the relative abundance of some soil-borne pathogens for T. grandis and P. sibiricum, indicating that this intercropping method may alleviate the impact of pathogens on crops, thus providing assistance for plant disease prevention and sustainable management.

Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation.

Asparagus cochinchinensis is a medicinal plant in China, which has gained attention owing its protective effect in human health. However, there are seldom studies to systematically reveal the rhizosphere bacterial community of A. cochinchinensis. In this study, we employed metagenomics and culturomics to analyze the bacterial community composition and diversity in continuous rhizosphere soil of A. cochinchinensis. Meanwhile, we assessed the effect of soil physicochemical properties on the bacterial community. Results showed that the most abundant TAXA is a taxon belonging to the family Streptomycetaceae, the genus Mycobacterium and the species Oligotropha carboxidovorans. The bacterial communities across various areas were similar. Significant differences of exchangeable magnesium and available phosphorus level were observed between three groups. Furthermore, bacterial community structure correlated closely with soil physicochemical properties. Additionally, a total of 103 strains were isolated and identified, representing 28 species. Based on this study, the rhizosphere bacterial community of A. cochinchinensis might influence its growth and development. The rhizosphere strains were isolated and their function request further investigation. This study firstly revealed the bacterial community in the A. cochinchinensis rhizosphere soil, providing valuable references for its quality improvement in practical cultivation process.

Microbial Community Structure, Diversity, and Succession During Decomposition of Kiwifruit Litters with Different Qualities

There are differences in the litter quality and decomposition rate of kiwifruit varieties, but it is not clear whether these differences are related to microbial communities. The leaf litters of two kiwifruit varieties (A. chinensis cv ‘Hongyang’ and A. chinensis cv ‘Jinyan’) were taken as objects, and the structure, diversity, and succession of the soil microbial communities were analyzed using an in situ decomposition experiment. Moreover, the contents of C, N, P, and K in the litters during decomposition were analyzed. The results show that there were variety differences in community structure at the generic level. Lophotrichus, Acaulium, and Fusarium were relatively more abundant in the microbial community of the ‘Hongyang’ kiwifruit litter, and Humicola and Tausonia were relatively more abundant in the microbial community of the ‘Jinyan’ kiwifruit litter. Subgroup_6 and Sphingomonas were the dominant bacteria. The bacterial community diversity of ‘Jinyan’ kiwifruit was higher than that of the ‘Hongyang’ kiwifruit litter. The community diversity was higher in the middle and later periods. The contents of C and N in the litters were the main factors affecting microbial communities. The abundances of Humicola and Apiotrichum were negatively correlated with the contents of C and N, and the abundances of Sphingomonas and SC-I-84 were positively correlated with the content of C. There were variety differences in the microbial communities corresponding to the decomposition processes of the ‘Hongyang’ and ‘Jinyan’ kiwifruit litters. The mechanisms of the variety differences were related to litter quality and the initial soil microbial community.

Bacterial community present in the earthworm’s gut and its role in soil biology and health

Earthworms are known as ecological engineers due to their significant role in enhancing soil health and productivity. Various factors such as temperature, moisture, acidity, pH, sunlight and the availability of organic matter influence their presence in soil. Earthworms exhibit diverse feeding and burrowing behaviors, which lead to crucial ecological processes within terrestrial ecosystems. Their interactions with soil result in the colonization of their gut and surrounding soil by diverse bacterial communities, including key species such as Escherichia coli, Streptomyces, Bacillus and Pseudomonas. These bacteria aid in the digestion of organic and inorganic matter, thereby altering soil physio-chemical properties and enhancing nutrient mineralization, which promotes plant growth. Additionally, earthworms influence nutrient cycling by modifying microbial soil populations and the bacterial communities in their gut and adjacent soil contribute to phytoremediation. This review delves into the types of bacterial populations found in the earthworm’s gut and surrounding soil, elucidating their specific roles and contributions to the terrestrial ecosystem. By understanding these complex interactions, we can better appreciate the vital role earthworms and their associated bacterial communities play in soil biology. This knowledge is essential for developing sustainable agricultural practices and improving soil management strategies, ultimately contributing to healthier and more productive ecosystems.

Bioorganic Fertilizer Can Improve Potato Yield by Replacing Fertilizer with Isonitrogenous Content to Improve Microbial Community Composition

The application of bio-organic fertilizers can significantly improve soil fertility and crop yield. This study explored how replacing bio-organic fertilizer with equal nitrogen affected potato quality, yield, and soil microbial diversity after a 4-year positioning experiment. The results showed that the application of bio-organic fertilizer instead of 70% chemical fertilizer could significantly increase potato yield by 10.4–155.4% but had no significant effect on quality. Furthermore, replacing chemical fertilizers with bio-organic fertilizers could decrease the number of soil bacterial species, but it did not influence the diversity of soil bacterial and fungal communities. At the phylum level, bio-organic fertilizer application was directly proportional to the abundance of Gemmatimonadota and Ascomycota, but inversely proportional to the abundance of Acidobacteriota and Basidiomycota. At the genus level, Longimicrobiaceae, Lysobacter, and Nocardioides were higher, whereas Vicinamibacteraceae, Gaiella, and Solirubrobacter were lower. Arthrobacter, Parcubacteria, Lautropia, Luteimonas, and Brunneochlamydosporium were the signatures of bio-organic fertilizer treatment and were positively correlated with the potato yield. Thus, in dry climates with little rainfall, partial substitution of chemical fertilizer with higher bioorganic fertilizers can alter the composition of microbial communities in potato rhizosphere soil, thus significantly improving potato yield.

Diversity, composition, and assembly processes of bacterial communities within per- and polyfluoroalkyl substances (PFAS)-contained urban lake sediments

Per- and polyfluoroalkyl substances (PFAS) are widespread, highly persistent, and bio-accumulative compounds that are increasingly found in the sediments of aquatic systems. Given this accumulation and concerns regarding the environmental impacts of PFAS, their influence on sedimentary bacterial communities remains inadequately studied. Here, we investigated the concentrations of 17 PFAS in sediments from six urban lakes in Nanjing, China, and assessed their effects on the diversity, composition, potential interactions, and assembly mechanisms of sedimentary bacterial communities. Sediment concentrations of PFAS ranged from 4.70 to 5.28 ng·g−1 dry weight. The high concentrations of the short-chain perfluorobutanesulfonic acid (PFBS) suggested its substitution for the long-chain perfluorooctanesulfonic acid (PFOS). As alternatives to long-chain PFAS, short-chain PFAS had similar effects on bacterial communities. The short-chain perfluoropentanoic acid (PFPeA) and the long-chain perfluorotridecanoic acid (PFTrDA) were the most important PFAS related to the ecological patterns of the co-occurrence network and may alter the composition of the sedimentary bacterial communities in the urban lakes. The Anaerolineaceae family represented as keystone bacteria within the PFAS-affected bacterial co-occurrence network. Deterministic processes (65.9 %), particularly homogeneous selection (63.2 %), were the dominant process driving bacterial community assembly. PFAS promoted the phylogenetic clustering and influenced the community dispersal capabilities to shape bacterial community assembly. This study provides a comprehensive analysis of PFAS distribution in sediments across six urban lakes in Nanjing and provides novel insights into the effects of PFAS on sedimentary bacterial communities. Further research is required to elucidate the mechanisms underlying the impacts of PFAS on microbial communities and to evaluate their broader ecological consequences.

Seasonal dynamics shaping bacterial community structure and networks in a Multi Geomorphological Unit System (MGUS) within the eastern Ulansuhai Lake Basin, North China

Different geomorphological units such as mountains, forests, fields, grasslands, sands and water, despite their distinct morphologies, are interconnected through micro-ecosystems that collectively maintain the balance of regional ecology. However, there is a lack of research concerning the spatial correlation among different landscape micro-ecosystems within a catchment area, hindering a comprehensive understanding of watershed systematic evolution across various landscape micro-ecosystems. To address this gap, seasonal variations in bacterial community structure and ecological network connectivity were investigated across different geomorphological units in the eastern Ulansuhai Lake Basin, North China. Water and soil samples were collected in May (beginning of the growing season, 23 samples) and November (end of the growing season, 20 samples) 2021. The diversity of bacterial communities within the Multi Geomorphological Unit System (MGUS) comprising “mountain, forest, field, grassland, sand and water” increased from May to November due to precipitation and human cultivation influences. Environmental characteristics, such as water and soil variations, exert a greater influence on bacterial community structure than differences in landscape units. The stability of the macro-ecological network structure within the MGUS was relatively high, with “water” playing a pivotal role in connectivity (the average betweenness centrality value of “water” was more than twice that of the other landscape samples). This led to the gradual emergence of deterministic processes in the construction of the bacterial community, shifting from stochastic processes (90.8 % drift effect in May) to biotic interactions (29.2 % heterogeneous selection in November). Furthermore, the bacterial community structure exhibited “macroscopic stability, with ‘water’ assuming a central role, while also showing microscopic variations, reflecting fluctuations in the contribution of dominant bacterial genera to the network structure over time”. Our study offers a core information analysis aimed at characterizing the temporal and spatial evolution of microbial community structure within an MGUS, thereby addressing a gap in microbial macroecology.

Production of polyhydroxybutyrate with photosynthetic bacteria treating artificial kitchen waste: Effect of light intensity

Kitchen waste can be used as a cheap carbon source for photosynthetic bacteria (PSB) to produce polyhydroxybutyrate (PHB). Light intensity is one of the most important factors in PSB growth. This paper investigated the efficiency and mechanism of PSB growth and PHB production from fermented kitchen waste under different light intensities. Results showed that PSB could grow well and produce PHB within the light intensity range of 1000-4000 lux using fermented kitchen waste as substrate. The 2000 lux was the optimal for PHB production, and PHB content and concentration reached 41.6% dry cell weight and 675.3mg/L, respectively, much higher than other light intensities. The corresponding PHB yield and productivity were 0.33g PHB/g chemical oxygen demand (COD) and 51.9mg/L/d, respectively. Removal of COD and NH4+ were 89.6% and 44.7%, respectively. Microbial community analysis showed that diversity and richness of bacterial community increased with time, and Rhodopseudomona and unclassified_f_Enterobacteriaceae were the dominant bacterial genera at the 2000 lux. Metabolic characteristics in fatty acid degradation, tricarboxylic acid cycle, pyruvate metabolism, photosynthesis, and pyruvate metabolism increased at the 2000 lux. Also, the key enzyme (PhaC, butyryl-CoA dehydrogenase, etc.) for synthesizing PHB was highly expressed, which corresponded to the large amount of PHB accumulation. This study provides a theoretical reference for treatment of kitchen waste with PSB for PHB production.

Bacterial community composition and metabolic characteristics of three representative Marine areas in northern China

Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.

Root, Nodule and Soil Bacterial Communities Associated With the Invasive Nitrogen-Fixing Lupinus polyphyllus.

Plants host microorganisms that can facilitate their success in becoming invasive. Established plant invasions might thus provide useful insights into potential changes in plant-associated microbiomes over the course of the invasion process. Here, we investigated the endophytic bacterial communities of the invasive herbaceous legume Lupinus polyphyllus, which is able to form mutualistic associations with N-fixing bacteria. More specifically, we examined the alpha diversity (observed bacterial taxa richness and Shannon diversity) and composition of bacterial communities in roots and nodules sampled from core and edge locations within 10 established invasion sites (> 10 years old) in southwestern Finland. Moreover, we compared the alpha diversity and structure of bacterial communities in the rhizosphere and bulk soil between core and edge locations within these invasion sites. We found that roots and nodules had distinctive endophytic bacterial communities, with roots having 24% higher bacterial alpha diversity (Shannon diversity) than nodules. In nodules, the dominant bacteria were assigned to the family Bradyrhizobiaceae, which includes N-fixing bacteria. Soil bacterial communities, instead, were shaped by soil type, with bulk soil hosting up to 27% higher alpha diversity (richness and Shannon diversity) than rhizosphere soil; however, there was no apparent difference in their community composition. Soil bacterial communities were only weakly associated with soil chemistry. Endophytic and soil bacterial communities did not differ between core and edge locations within the established invasions. Our findings suggest that L. polyphyllus may not induce dramatic changes in the bacterial communities with which it associates over the course of the local invasion process.

Response of bacterial communities in desert grassland soil profiles to acid mine drainage pollution

Acid mine drainage (AMD) causes serious environmental pollution, which imposes stresses on soil ecosystems. Therefore, it is critical to study the responses of soil bacterial communities to AMD pollution in ecologically fragile desert grasslands. Here, the bacterial community composition, structure, and assembly processes in vertical soil profiles of an AMD contaminated desert grassland were explored using 16S rRNA high-throughput sequencing. The results showed that the surface layers of the profiles exhibited lower pH and higher heavy metals (HMs) content due to AMD influence. The AMD contamination led to reduced bacterial diversity in the surface soil layer of the profiles and significantly changed the bacterial community composition and structure. Gradients in pH, TK, TN, and HMs were the main factors driving bacterial community variability. In contrast to the uncontaminated profile, deterministic processes were important in shaping soil bacterial community in the AMD contaminated profiles. These findings will enhance understanding about the responses of soil bacteria in desert grassland soil to the environmental changes caused by AMD contamination and will improve the remediation of AMD contaminated soil.