Variation In Bacterial Diversity Research Articles

Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp.

The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium.

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

Contrasting patterns for bacteria and archaea in response to salt stress across alpine wetlands of the Tibetan Plateau

Understanding microbial responses to environmental stress is crucial for comprehending their distribution and supporting conservation efforts. Yet, comprehensive evaluations of these responses across diverse microbial taxa within the framework of classical ecological theories are scarce. This gap limits our ability to predict the impact of environmental changes on the diversity and functions of soil microbes in natural settings. In this study, we conducted a field survey across twenty alpine wetlands on the Tibetan Plateau. Employing amplicon sequencing with network theories, we investigated the biodiversity and coexistence of bacteria and archaea under a wide range of natural salinity conditions. Our results demonstrated a linear decrease in bacterial diversity with increased salinity, while archaeal diversity showed a non-linear pattern, initially declining and then rising, reflecting varied adaptation strategies to salt stress. Network analysis revealed a heightened complexity in positive associations among bacteria under salt stress. In contrast, archaea exhibited a decrease in both positive and negative associations, with the community succession to halophiles. These results imply that bacteria may counteract stress through enhanced facilitation, whereas archaea predominantly rely on stress-tolerant taxa. Additionally, structural equation modeling confirmed our hypothesis regarding the ecological response strategies of bacteria and archaea to salinity stress, showing that the variation in bacterial diversity is mainly explained by the complexity of positive associations, whereas archaeal diversity directly correlates with salinity levels. Overall, this study offers novel insights into the ecological strategies of prokaryotes under salinity stress and enriches our understanding of the processes maintaining microbial diversity in stressful conditions.

Variations in bacterial diversity and community structure in the sediments of an alkaline lake in Inner Mongolia plateau, China.

Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos' desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = -0.924, p < 0.01; r = -0.800, p < 0.01; r = -0.933, p < 0.01) and salinity (r = -0.615, p < 0.05; r = -0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.

Temperature and phosphorus: the main environmental factors affecting the seasonal variation of soil bacterial diversity in Nansi Lake Wetland.

The soil bacteria promote the circulation conversion of lake nutrients and play an important role in maintaining the balance of the lake ecosystem. Few studies have investigated the association of seasonal variation in bacteria and environmental factors in inland freshwater lake wetlands. Nansi Lake is a large shallow freshwater lake in northern China. It is an important hub of the eastern route of the South-to-North Water Diversion Project. In this study, bacterial 16S rRNA genes were used to analyze the variation of soil bacterial community diversity in Nansi Lake Wetland and its influencing factors in different seasons. It is showed that the phylum, family, and genus with the largest relative abundance in the soil of Nansi Lake Wetland are Proteobacteria, Nitrosomonadaceae, and MND1, respectively. There were significant seasonal differences in soil bacterial diversity in Nansi Lake Wetland, which was significantly higher in summer than in winter. Seasonal variation in environmental factors was significantly correlated with the variation in bacterial communities. Temperature and the content of available phosphorus may be the key factors influencing seasonal variation in bacterial diversity. The results of this study further enhance our understanding of the relationship between bacterial community diversity and environmental factors in the lake wetland ecosystem, which can provide scientific data for the conservation of Nansi Lake Wetland.

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties.

Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

Effects of Combined Application of Fungal Residue and Chemical Fertilizer on Soil Microbial Community Composition and Diversity in Paddy Soil

Fungal residue is a unique abundant organic material undervalued in agricultural production. The application of chemical fertilizer combined with fungal residue can not only improve soil quality but also regulate the microbial community. However, it is unclear whether the response of soil bacteria and fungi to the combined application of fungal residue and chemical fertilizer is consistent. Therefore, a long-term positioning experiment in a rice field was conducted with a total of nine treatments. Chemical fertilizer (C) and fungal residue (F) were applied at 0, 50%, and 100% to evaluate 1 the change in soil fertility properties and microbial community structure and 2 the main driving factors of soil microbial diversity and species composition. The results showed that soil total nitrogen (TN) was highest after treatment C0F100 (55.56% higher than in the control), and the carbon to nitrogen ratio (C/N), total phosphorus (TP), dissolved organic carbon (DOC), and available phosphorus (AP) contents were highest after treatment with C100F100(26.18%, 26.46%, 17.13%, and 279.54% higher than in the control, respectively). The amounts of soil organic carbon (SOC), available nitrogen (AN), available potassium (AK), and pH were highest after treatment with C50F100 (85.57%, 41.61%, 29.33%, and 4.62% higher than in the control, respectively). Following the application of fungal residue with chemical fertilizer, there were significant changes in the α-diversity of bacteria and fungi in each treatment. Compared with that of the control (C0F0), different long-term applications of fungal residue with chemical fertilizer did not significantly change soil bacterial β-diversity but resulted in significant differences in fungal β-diversity, and the relative abundance of soil fungal Ascomycota and Sordariomycetes significantly decreased after the application of C50F100. The random forest prediction model indicated that AP and C/N were the main driving factors of bacterial and fungal α-diversity, respectively, and AN, pH, SOC, and DOC were the main driving factors of bacterial β-diversity, whereas AP and DOC were the main driving factors of fungal β-diversity. Correlation analysis suggested that the relative abundance of soil fungal Ascomycota and Sordariomycetes had a significantly negative correlation with SOC, TN, TP, AN, AP, AK, and C/N. PERMANOVA showed that variation in soil fertility properties, dominant species of soil bacteria at the phylum and class level, and dominant species of soil fungi at the phylum and class level were all best explained by fungal residue (46.35%, 18.47%, and 41.57%, respectively), and variation in bacterial diversity was best explained by fungal residue (23.84%) and to a lesser extent by the interaction between fungal residue and chemical fertilizer (9.90%). In contrast, the variation in fungal diversity was best explained by the interaction between fungal residue and chemical fertilizer (35.00%) and to a lesser extent by fungal residue (10.42%). In conclusion, the application of fungal residue has more advantages than chemical fertilizer in influencing soil fertility properties and microbial community structure changes.

Spatiotemporal variations, assembly processes, and co-occurrence patterns of particle-attached and free-living bacteria in a large drinking water reservoir in China.

Particle-attached (PA) and free-living (FL) bacterial communities are sensitive to pollutant concentrations and play an essential role in biogeochemical processes and water quality maintenance in aquatic ecosystems. However, the spatiotemporal variations, assembly processes, co-occurrence patterns, and environmental interactions of PA and FL bacteria in drinking water reservoirs remain as yet unexplored. To bridge this gap, we collected samples from 10 sites across four seasons in Lake Tianmu, a large drinking water reservoir in China. Analysis of 16S rRNA gene libraries demonstrated spatiotemporal variations in bacterial diversity and identified differences in bacterial community composition (BCC) between PA and FL lifestyles. Capacity for nitrogen respiration, nitrogen fixation, and nitrate denitrification was enriched in the PA lifestyle, while photosynthesis, methylotrophy, and methanol oxidation were enriched in the FL lifestyle. Deterministic processes, including interspecies interactions and environmental filtration, dominated the assembly of both PA and FL bacterial communities. The influence of environmental filtration on the FL community was stronger than that on the PA community, indicating that bacteria in the FL lifestyle were more sensitive to environmental variation. Co-occurrence patterns and keystone taxa differed between PA and FL lifestyles. The ecological functions of keystone taxa in the PA lifestyle were associated with the supply and recycling of nutrients, while those in FL were associated with the degradation of complex pollutants. PA communities were more stable than FL communities in the face of changing environmental conditions. Nutrients (e.g., TDN and NO3 -) and abiotic and biotic factors (e.g., WT and Chl-a) exerted positive and negative effects, respectively, on the co-occurrence networks of both lifestyles. These results improve our understanding of assembly processes, co-occurrence patterns, and environmental interactions within PA and FL communities in a drinking water reservoir.

Cultivation in an Alpine Region: Implications for Soil Bacteria

Land use change is a major predictor for variations in soil bacteria, which plays a key role in maintaining soil multifunctionality and function of terrestrial ecosystems. The effects of land use change on the soil bacterial community in an alpine region at the Qinghai-Tibetan Plateau (QTP) were still unclear. In this study, we investigated soil bacterial profiles under grazed grassland, enclosed grassland, continuous cropland, rotation cropland and abandoned cropland in the Tianzhu alpine agro-pastoral ecotone. Our results showed that Proteobacteria, Acidobacteria and Actinobacteria were the most three abundant phyla regardless of land use change, accounting for over 60% of the total. Cultivation declined soil bacterial alpha diversity without recovering even after abandonment. Over 73% variations in bacterial diversity can be explained by soil physical and chemical properties. In addition, soil moisture could be the main driver for the difference in bacterial structure between croplands and others. Soil bulk density, pH, organic carbon and total nitrogen contents seem to be the key factors determining the difference in bacterial structure between abandoned croplands and others. Our results have implications for comprehensive understanding about the responses of the soil bacterial community to land use change in alpine regions.

Integrating pH into the metabolic theory of ecology to predict bacterial diversity in soil.

Microorganisms play essential roles in soil ecosystem functioning and maintenance, but methods are currently lacking for quantitative assessments of the mechanisms underlying microbial diversity patterns observed across disparate systems and scales. Here we established a quantitative model to incorporate pH into metabolic theory to capture and explain some of the unexplained variation in the relationship between temperature and soil bacterial diversity. We then tested and validated our newly developed models across multiple scales of ecological organization. At the species level, we modeled the diversification rate of the model bacterium Pseudomonas fluorescens evolving under laboratory media gradients varying in temperature and pH. At the community level, we modeled patterns of bacterial communities in paddy soils across a continental scale, which included natural gradients of pH and temperature. Last, we further extended our model at a global scale by integrating a meta-analysis comprising 870 soils collected worldwide from a wide range of ecosystems. Our results were robust in consistently predicting the distributional patterns of bacterial diversity across soil temperature and pH gradients-with model variation explaining from 7 to 66% of the variation in bacterial diversity, depending on the scale and system complexity. Together, our study represents a nexus point for the integration of soil bacterial diversity and quantitative models with the potential to be used at distinct spatiotemporal scales. By mechanistically representing pH into metabolic theory, our study enhances our capacity to explain and predict the patterns of bacterial diversity and functioning under current or future climate change scenarios.

Nitrogen use aggravates bacterial diversity and network complexity responses to temperature

Rising temperature affects microbial composition and function in agriculture field, especially under nitrogen fertilization. In this study, we investigated the bacterial community of paddy soil incubated at controlled temperatures (5 °C, 15 °C, 25 °C, and 35 °C). Results showed that the response of bacterial communities to temperature was not uniform. Temperature elevation from 15 to 25 °C abruptly shifted the soil bacterial community, whereas elevation from 5 to 15 °C and from 25 to 35 °C had a marginal effect. The bacterial α-diversity was higher at 5 °C and 15 °C, owing to the massively distributed taxa with low abundance. However, as the temperature increased to 25 °C and 35 °C, these taxa were diminished, whereas Firmicutes significantly increased, resulting in a strong decline in α-diversity. Simultaneously, bacterial network complexity significantly increased at 25 °C and 35 °C, indicating the bacteria had closer interactions. Nitrogen application aggravated the variation in bacterial diversity and network complexity among temperatures. Interestingly, most complex network was observed under higher temperatures in fertilized soils. Collectively, these results indicate that nitrogen exacerbates the response of the soil bacterial community to temperature, and association between diversity and network complexity may be present.

Nitrogen Enrichment Reduces the Diversity of Bacteria and Alters Their Nutrient Strategies in Intertidal Zones

Intertidal ecosystems are affected by severe nitrogen (N) pollution as a result of anthropogenic activities, and it is unclear how this may affect intertidal microbial communities, which play critical roles in regulating biogeochemical cycles. To address this gap, we conducted a two-month mesocosm experiment using six targeted concentrations of total N. The findings indicated that N entering seawaters has direct negative effects on the bacterial diversity. Dose dependence was found for the effects of N on bacterial diversity in sediment: low N addition increased the bacterial diversity, but a reduction in bacterial diversity occurred when N exceeded a certain value (≥ 3 mg L−1). Additionally, N enrichment caused clear shifts in bacterial community composition with increases in the relative abundance of Balneola (organic-degrading), Phalacroma mitra (carbohydrate-fermenting), and Bacteroides (phosphorus (P)-solubilizing), and decreases in Leptolyngbya_PPC_6406 (N2-fixing). The increased abundance in P-solubilizing and organic-degrading bacteria and decrease in N-fixing bacteria, combined with the upregulated activity of alkaline phosphatase and downregulation of urease activity, implied that the bacterial assemblage tended to be more effective in P and carbon acquisition but reduced N acquisition. Further path analysis suggested that N had direct effects on bacteria and contributed 50%–100% to the variations in bacterial diversity, whereas environmental changes such as dissolved oxygen and pH played minor roles. Overall, bacteria occurring in sediment were likely more stress-resistant to high N exposure than those occurring in seawater, possibly due to the high buffering capacity of sediment and growth tolerances of bacteria in the sediment. These findings point to the vulnerability of microbes in water systems to increasing global N loading, and that N reduction is needed to combat the loss of microbial diversity.

Identification and Analysis of Gut Microbiota and Functional Metabolism in Decompensated Cirrhosis with Infection.

Intestinal dysbiosis play a role in the adverse outcomes of sepsis and septic shock. However, variations in bacterial diversity and microbiota-related functional metabolic alterations within the gut microbiome in decompensated cirrhosis (DC) patients with infection remain unknown. We conducted 16-srRNA sequencing on stool samples (n=51: sepsis, 27/no sepsis, 24) collected from consecutive DC patients upon admission. Bacterial diversity, significant taxa, and respective metabolic profiling were performed based on subgroup comparisons. Conet/Cytoscape was utilized to identify significant non-random patterns of bacterial copresence and mutual exclusion for clinical events. Genera associated with pathogenicity in conditions of immune exhaustion (Corynebacterium, Lautropia) were predominant in patients with sepsis. Metabolic pathways associated with oxidative stress and endotoxemia [lipopolysaccharide (LPS) synthesis and sulfur relay] were significantly upregulated in sepsis. Specific taxa were associated with sites of infection in DC patients. Protective oxidant pathways that increase glutathione were upregulated in those without sepsis. Gammaproteobacteria family of sulfur-metabolizing bacteria, exaggeration of orally predominant pathogens (Prevotella), and pathways of severe LPS-related hyperinflammatory stress were notable in those with interleukin-6 levels >1,000 pg/dL. Pathogenic genera related to an immune deficient state was significant in DC with ≥2 infection episodes. Megamonas was associated with survival during the same admission. Specific gut microbiota and their metabolites were associated with sepsis and related events in patients with DC. Identifying beneficial strains that reduce immune exhaustion and supplementation of favorable metabolites could improve therapeutics for DC and sepsis, for which larger prospective, well controlled population-based studies remain an unmet need.

The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines.

SummarySeed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant‐related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.

Temporal variation in bacterial community profile on patients' bedsheets in a primary healthcare unit.

Fabrics serve as fomites in spreading nosocomial infections. As a patient is in close contact with bedsheets, it is important to assess the seasonal variation in bacterial diversity on these in healthcare units. The study was conducted to characterise the bacterial diversity on patients' bedsheets across 7months in a primary healthcare unit. Polyester-cotton blend fabric was stitched on bedsheets, and temporal dynamics of bacterial communities was assessed from May to November 2019. qPCR and amplicon sequencing of 16S rRNA gene was performed for profiling of bacterial community. Results revealed the dominance of Bacillota followed by Pseudomonadota, and Actinomycetota. A seasonal variation was observed in the bacterial load, with maximum values in June. This indicates the impact of environmental conditions on bacterial abundance and composition on fabrics in healthcare unit. The presence of priority pathogens on the patient bedsheets is a human health concern reiterating the need for season-specific laundering protocol.

Allometric releases of nitrogen and phosphorus from sediments mediated by bacteria determines water eutrophication in coastal river basins of Bohai Bay

Although the Chinese government has conducted much work in recent years to reduce land-based pollutant discharge, eutrophication continues to occur frequently in many rivers, estuaries, and coastal waters. This may indicate that sediment is a major source rather than a sink for nitrogen (N) and phosphorus (P). To clarify the endogenous mechanisms of eutrophication in coastal river basins, the eutrophication status, physicochemical properties, and bacterial parameters of overlying waters and sediments in the catchment (CA), estuarine (EA), and offshore (OA) areas in the Duliujian River Basin of Bohai Bay were investigated. The results showed that the eutrophication index (EI) of CA, EA, and OA were 62.71, 57.86, and 36.51, respectively. The EI was more sensitive to increases in P (slope = 3.887) than to increases in N (slope = 0.734) of the overlying water, indicating that P is the main factor driving eutrophication in the coastal river basin. However, a nonlinear relationship was found between P in sediments and overlying waters, suggesting that bacterial mediation may occur during P release. As speculated in this study, P in the overlying water increased more quickly than N with increasing bacterial diversity and metabolic abundance, indicating that the allometric release of N and P mediated by bacteria increases the risk of eutrophication. Redundancy analysis showed that organic matter and total N in sediment have positive effects on bacterial communities, which explains 21.8% and 23.7% variation in bacterial diversity, and explains 31.3% and 7.1% variation in bacterial metabolism. This also suggests that the accumulation of N in the sediment promotes the release of P and further aggravates the eutrophication of water. Therefore, simultaneous control of N and P is necessary to control water eutrophication in coastal river basins.

The carbon and nitrogen stoichiometry in litter-soil-microbe continuum rather than plant diversity primarily shapes the changes in bacterial communities along a tropical forest restoration chronosequence

Soil bacteria play core roles in mediating the functional linkage between above- and belowground components during forest restoration. However, the pattern and mechanism through which plants and soils influence bacterial communities remain unclear. This study aimed to quantify the contributions of plant community and soil characteristics to shifts in bacterial composition and diversity along a tropical forest restoration chronosequence in the Xishuangbanna. We found a negative effect of forest restoration on bacterial composition and a positive impact on the diversity. Forest restoration changed bacterial communities from being oligotrophic Acidobacteria and Actinobacteria dominatedto copiotrophic Proteobacteria and Firmicutes dominated. Forest restoration also induced a 1.5–1.6 fold increase in OTU richness and diversity of bacterial communities. Soil variables, including plant litter, contributed 46.3–58.1% to the variations in bacterial composition and diversity, while the contribution of plant community was 6.4–13.8%. Furthermore, the increase in plant richness and diversity had minor contribution to variations in bacterial diversity and composition during forest restoration. Soil bacterial diversity was primarily explained by the elevated levels of carbon and nitrogen stoichiometry in the litter-soil-microbe continuum, but litter was explained by the increased plant diversity. In contrast, soil bacterial composition was negatively correlated with biomass, nitrogen, and carbon:nitrogen of the litter, as well as the level of soil carbon and nitrogen pools. Our data suggested that the carbon and nitrogen stoichiometry in litter-soil-microbe continuum rather than plant diversity primarily shaped the changes in bacterial composition and diversity along tropical forest restoration.

Response of a Coastal Microbial Community to Olivine Addition in the Muping Marine Ranch, Yantai

Spreading olivine powder in seawater to enhance alkalinity through weathering reactions has been proposed as a potential solution to control atmospheric CO2 concentration. Attention has usually been paid to the chemical properties of seawater after the addition of olivine within lab and modeling studies. However, both microbial acclimation and evolution in such manipulated natural environments are often overlooked, yet they are of great importance for understanding the biological consequences of whether olivine addition is a feasible approach to mitigating climate change. In this study, an olivine addition experiment was conducted to investigate variation in bacterial diversity and community composition in the surface and bottom seawater of a representative marine ranch area in the Muping, Yantai. The results show that the composition of the particle-attached microbial community was particularly affected by the application of olivine. The relative abundance of biofilm-forming microbes in particle-attached fraction increased after the addition of olivine, while no significant variation in the free-living bacterial community was observed. Our study suggests that olivine addition would reshape the bacterial community structure, especially in particle-attached microenvironments. Therefore, the risk evaluation of alkalinity enhancement should be further studied before its large-scale application as a potential ocean geoengineering plan.

Bacterial diversity and community composition in lake water and sediment of Lake Daihai

采用高通量测序技术，研究了内蒙古岱海流域入湖河流、湖水及沉积物细菌多样性及群落组成.结果显示，细菌多样性从高到低依次为：沉积物>河流>湖泊.聚类分析表明入湖河流、湖水和沉积物细菌群落可分为明显不同的3支，说明这3种生境中细菌群落结构有较大差异.物种注释结果表明，河流中优势细菌菌群为髌骨细菌（Patescibacteria）、变形菌门（Proteobacteria）、拟杆菌门（Bacteroidetes）和放线菌门（Actinobacteria）；湖水中优势细菌菌群为放线菌门（Actinobacteria）；而沉积物中优势细菌菌群为变形菌门和绿弯菌门（Chloroflexi）.典范对应分析及Monte Carlo检验表明，电导率和悬浮物含量对水体中（河流与湖泊）细菌群落影响显著，二者共解释了细菌群落变化的86.5%；而冗余分析及Monte Carlo检验表明，泥深、磁化率和总有机碳对沉积物中细菌群落影响显著，三者共解释了细菌群落变化的47.9%.近30年来，岱海地区气候变化和人类活动导致湖水咸化，沉积物碳氮指标显著增长.岱海水体及沉积物细菌多样性及群落组成的差异及其主要驱动因子，反映了细菌对这种气候变化和人类活动共同作用的响应.;Bacterial diversity and community composition was investigated in the Lake Daihai Basin, Inner Mongolia using high-throughput sequencing technology. The results showed that bacterial diversity was highest in sediments, followed by river and lake water. Cluster analysis showed that bacterial community compositions in the inflowing river, lake water and sediments were separated into three distinct groups, indicating great differences in bacterial community compositions among the three habitats. Taxonomic annotation showed that the dominant bacterial flora in the river was Patescibacteria, Proteobacteria, Bacteroidetes and Actinobacteria. Actinobacteria was the most dominant bacteria phylum in the lake water, while the dominant bacterial flora in sediments were Proteobacteria and Chloroflexi. Canonical correspondence analysis and Monte Carlo permutation test revealed that the variations of bacterial community compositions in the river and lake were significantly explained by conductivity and suspended solids, which explained 86.5% of the variation. Redundant analysis and Monte Carlo permutation test revealed that the variations of bacterial community compositions in sediment were significantly explained by depth, magnetic susceptibility and total organic carbon, which explained 47.9% of the variation in total. During the past 30 years, Lake Daihai has experienced salinization in lake water and a remarkable increase of carbon and nitrogen in the sediment due to climate change and anthropogenic activities. The variations of bacterial diversity and community composition in the water and sediments, as well as their main driving environmental factors, highlight the responses of bacteria to the combined effects of climate change and anthropogenic activities on Lake Daihai.

Impact of salt concentration on bacterial diversity and changes in biogenic amines during fermentation of farmhouse soybean paste in Northeast China

Farmhouse soybean paste in Northeast China is a traditional fermented product made from soybean, and more than 11% (w/w) salt is usually added during production to control the fermentation process. In this study, the variations in bacterial diversity, biogenic amines(BAs) and physicochemical properties during the natural fermentation of soybean paste with different salt concentrations (8%, 9%, 10%, 11%, and 12%) were studied. The results show that at 0 days (0 d) of fermentation in soybean paste, the dominant genera included Staphylococcus, unidentified Clostridiales, and Sporolactobacillus. During fermentation from 30 d to 90 d, the dominant genera were Tetragenococcus and Staphylococcus. However, the proportions of the dominant genera were different depending on the salt concentration. Putrescine(Put), tryptamine(Try), β-phenethylamine(Phe), cadaverine(Cad), histamine(His), and tyramine(Tyr) showed negative correlations with salt concentration. The amino type nitrogen(ANN), titratable acidity(TTA) and total number of colonies were also negatively correlated with salt concentration. Analysis of the correlation between genera and BAs showed that 12 genera were positively correlated with BAs, and 4 genera were negatively correlated with BAs. The results of this study indicated that salt has a significant impact on bacterial diversity during the fermentation of soybean paste, which in turn affects the changes in bacterial metabolites. From the perspective of food safety, the amount of salt added in the soybean paste can be reduced to 10% under the existing fermentation conditions.