Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake

Polysaccharide from Atractylodes macrocephala Koidz Binding with Zinc Oxide Nanoparticles as a Novel Mucosal Immune Adjuvant for H9N2 Inactivated Vaccine

H9N2 avian influenza poses a significant public health risk, necessitating effective vaccines for mass immunization. Oral inactivated vaccines offer advantages like the ease of administration, but their efficacy often requires enhancement through mucosal adjuvants. In a previous study, we established a novel complex of polysaccharide from Atractylodes macrocephala Koidz binding with zinc oxide nanoparticles (AMP-ZnONPs) and preliminarily demonstrated its immune-enhancing function. This work aimed to evaluate the efficacy of AMP-ZnONPs as adjuvants in an oral H9N2-inactivated vaccine and the vaccine's impact on intestinal mucosal immunity. In this study, mice were orally vaccinated on days 0 and 14 after adapting to the environment. AMP-ZnONPs significantly improved HI titers, the levels of specific IgG, IgG1 and IgG2a in serum and sIgA in intestinal lavage fluid; increased the number of B-1 and B-2 cells and dendritic cell populations; and enhanced the mRNA expression of intestinal homing factors and immune-related cytokines. Interestingly, AMP-ZnONPs were more likely to affect B-1 cells than B-2 cells. AMP-ZnONPs showed mucosal immune enhancement that was comparable to positive control (cholera toxin, CT), but not to the side effect of weight loss caused by CT. Compared to the whole-inactivated H9N2 virus (WIV) group, the WIV + AMP-ZnONP and WIV + CT groups exhibited opposite shifts in gut microbial abundance. AMP-ZnONPs serve as an effective and safe mucosal adjuvant for oral WIV, improving cellular, humoral and mucosal immunity and microbiota in the gastrointestinal tract, avoiding the related undesired effects of CT.

Age, growth, maturity and mortality of the tapetail anchovy Coilia brachygnathus (Engraulidae) in Lake Honghu, China

The tapertail anchovy Coilia brachygnathus, a commercially important species mainly distributed along the mid-lower Chang-Jiang basin, is by far the most dominant species in Lake Honghu. To figure out its success in this semiclosed lake, some basic biological parameters of this anchovy were analysed based on samples seasonally collected from October 2020 to December 2021. The results demonstrated that the age classes of fished individuals varied from 0.5 to 3.5, with the majority (97.36%) being between 0.5 and 3 years old. The size at 50% maturity of 17.2 cm total length (TL) for females and 19.0 cm TL for males corresponded to 1 and 1.6 years, respectively. Coilia brachygnathus has a short life span, early sexual maturity and a relatively fast growth rate. The flourishing of the fish in the lake is mainly attributed to its short life span, early maturity, fast growth rate, closed fishing, pelagic spawners, the availability of plenty of food and low predation effect on it. Age 3.5 year occurs in an extremely small percentage of the total (<3%), indicating that a large number of larger-sized or older fish died after spawning, which is probably one of the major sources of water pollution if the closed fishing measure is adopted in Lake Honghu. Thus, individuals older than 2 years or more than 20.0 cm TL should be harvested. These findings have important management implications for the fish resources in Lake Honghu and beyond.

Similar assembly mechanisms but distinct co-occurrence patterns of free-living vs. particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu

Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.

Water Quality and Microbial Community in the Context of Ecological Restoration: A Case Study of the Yongding River, Beijing, China

Ecological water replenishment via interbasin water diversion projects provides opportunities for ecological river restoration. Untangling water quality changes, microbiota dynamics, and community functions is necessary for sustainable ecological management. Using the Yongding River as a case study, we monitored the water quality and applied genomic sequencing to investigate microbial communities of the river in different stages after ecological water replenishment. Our results showed that river water quality represented by chemical oxygen demand (COD), total nitrogen (TN), and chlorophyll-a (Chl-a) did not change significantly during months after water replenishment. The bacterial community composition varied in different months and river subsections. The Cyanobium_PCC-6307, CL500-29 marine group, and Pseudomonas were dominant in the later stages after water replenishment. Water temperature, pH, and nutrient levels significantly affected the microbial community composition, and ecological restoration may have the potential to influence nitrogen cycling in the river. Our results can provide ecological insights into sustainable water quality maintenance and river management following ecological restoration enabled by ecological water replenishment.

Antibiotic resistance genes and their links with bacteria and environmental factors in three predominant freshwater aquaculture modes

Rapid development of aquaculture industry and increasing demand of various inputs (especially antibiotics), are suspected to promote the occurrence and spread of ARGs in aquaculture related environments. However, the occurrences of ARGs under different freshwater aquaculture practices are rarely known. Here, we investigated the seasonal profiles of the main ARGs, intI1 and bacteria in waters from three kinds of predominant freshwater aquaculture practices around the Honghu Lake (China), as well as their co-occurrences and interrelationships with antibiotics, heavy metals and general water quality. The results indicate that quinolone resistance genes (qnrB), tetracycline resistance genes (tetB and tetX) and sulfonamide resistance genes (sul1 and sul2) were the top five predominant ARGs with seasonal variations of abundance. Fish ponds were of the highest absolute abundances of tested ARGs than the other two modes. Crayfish ponds and their adjacent ditches shared similar ARGs profile. Different subtypes of ARGs belonging to the same class of resistance were varied in abundances. Some bacteria were predicted to carry different ARGs, which indicating multi-antibiotic resistances. Moreover, the combined environmental factors (antibiotics, heavy metals and water quality) partially shaped the profiles of ARGs and bacteria composition. Overall, this study provides new comprehensive understanding on the characterization of ARGs contamination in different freshwater aquaculture practices from the perspectives of environmental chemistry, microbiology and ecology. The results would benefit the optimization of aquaculture practices toward environmental integrity and sustainability.

Sustainability of the rice-crayfish co-culture aquaculture model: microbiome profiles based on multi-kingdom analyses

While the rice-crayfish culture (RCFP) model, an important aquaculture model in Asia, is generally considered a sustainable model, its sustainability in terms of microbial community profiles has not been evaluated. In this study, multi-kingdom analyses of microbiome profiles (i.e., bacteria, archaea, viruses, and eukaryotes) were performed using environmental (i.e., water and sediment) and animal gut (i.e., crayfish and crab gut) microbial samples from the RCFP and other aquaculture models, including the crab-crayfish co-culture, crayfish culture, and crab culture models, to evaluate the sustainability of the RCFP systematically. Results showed that RCFP samples are enriched with a distinct set of microbes, including Shewanella, Ferroplasma, Leishmania, and Siphoviridae, when compared with other aquaculture models. Additionally, most microbes in the RCFP samples, especially microbes from different kingdoms, were densely and positively connected, which indicates their robustness against environmental stress. Whereas microbes in different aquaculture models demonstrated moderate levels of horizontal gene transfer (HGT) across kingdoms, the RCFP showed relatively lower frequencies of HGT events, especially those involving antibiotic resistance genes. Finally, environmental factors, including pH, oxidation-reduction potential, temperature, and total nitrogen, contributed profoundly to shaping the microbial communities in these aquaculture models. Interestingly, compared with other models, the microbial communities of the RCFP model were less influenced by these environmental factors, which suggests that microbes in the latter have stronger ability to resist environmental stress. The findings collectively reflect the unique multi-kingdom microbial patterns of the RCFP model and suggest that this model is a sustainable model from the perspective of microbiome profiles.

Glycyrrhiza uralensis Fisch. Root-associated microbiota: the multifaceted hubs associated with environmental factors, growth status and accumulation of secondary metabolites

Glycyrrhiza uralensis Fisch. is an important, perennial medicinal plant whose root microbiome is considered to play an important role in promoting accumulation of effective medicinal ingredients (liquiritin and glycrrhizic acid). Here, we report a comprehensive analysis of the microbial community structural composition and metabolite-plant-microbes association of G. uralensis Fisch. We collected both soil and rhizosphere samples of G. uralensis from different environmental conditions (cultivated and wild) and growth years (grown for one year and three years). Our data revealed higher species diversity in the wild group than in the cultivated group. The core rhizosphere microbiome of G. uralensis comprised 78 genera, including Bacillus, Pseudomonas, Rhizobium, some of which were potential plant beneficial microbes. Our results suggest that the growth of G. uralensis has a correlation with the root-associated microbiota assemblage. Integrated analysis among rhizosphere microbial taxa, plant gene expressions, and liquiritin and glycrrhizic acid accumulation showed that the liquiritin and glycrrhizic acid accumulation exhibited associations with the rhizosphere microbial composition at the genus level. The results provide valuable information to guide cultivation of G. uralensis, and potentially to harness the power of the root-associated microbiota to improve medicinal plant production.

Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment

The increasing pollution of urban drinking water sources by antibiotic resistance genes (ARGs) threatens human health worldwide. However, the distribution and influencing factors of ARGs, especially how to reveal the risks of ARGs in this environment remains unclear. Hence, Chaohu Lake was selected as an example to investigate the characteristics of ARGs and explore the interactions among physicochemical factors, microorganisms, and ARGs by metagenomic approach. In this work, 75 ARG subtypes with an average of 30.4 × /Gb (ranging from 15.2 ×/Gb to 57.9 ×/Gb) were identified, and multidrug and bacA were most frequent in Chaohu Lake. Non-random co-occurrence patterns and potential host bacteria of ARGs were revealed through co-occurrence networks. Microbial community and mobile genetic elements (MGEs) were the major direct factors in ARG profiles. The dissemination of ARGs was mainly driven by plasmids. Considering the interactions among MGEs, human bacterial pathogens, and ARGs, antibiotic resistome risk index (ARRI) was proposed to manifest the risks of ARGs. Overall, our work systemically investigated the composition and associated factors of ARGs and built ARRI to estimate the potential risks of ARGs in a typical urban drinking water source, providing an intuitive indicator for managing similar lakes.

Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework

It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as "multitask" bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.

Mechanisms of niche-neutrality balancing can drive the assembling of microbial community

One hotspot of present community ecology is to uncover the mechanisms of community succession. In this study, two popular concepts, niche-neutrality dynamic balancing and co-occurrence network analysis, were integrated to investigate the dispersal dynamics of microbial communities in a freshwater river continuum in subtropical China. Results showed that when habitat conditions were mild and appropriate, such as in the clean upstream river, free of heavy pollution or long-lasting extreme disturbances, stochastic processes could increase species diversities, and organize communities into relatively loosely linked and stable networks with higher modularity and more modules. However, when conditions became degraded under heavy pollution, the influence of neutrality diminished, and niche-based selection imposed more constraints on communities and guided the assembling processes in certain directions: depleting species richness, strengthening interspecies connections and breaking boundaries of modules. Consequently, communities became more sensitive to fluctuations so as to deal with the harsh conditions efficiently. Another interesting finding was that, both as keystone taxa of communities, module hubs were mostly neutrally distributed generalists with high abundances, and were beneficial to many related operational taxonomic units. In contrast, connectors were less abundant and their distributions were more subjected to the environments. Therefore, connectors were probably responsible for the information transmission between microbial communities and environments, as well as between different modules, and thus could restrict the dispersal of microbes and guide the direction of community assembly.

Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China

Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO₄^2–)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.

Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes

Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.

Diversity patterns of soil microbial communities in the Sophora flavescens rhizosphere in response to continuous monocropping

Background

Continuous monocropping can affect the physicochemical and biological characteristics of cultivated soil. Sophora flavescens is a valuable herbal medicine and sensitive to continuous monocropping. Currently, diversity patterns of soil microbial communities in soil continuous monocropping with S. flavescens have not been extensively elucidated.

Results

In this study, comparative 16S rDNA and internal transcribed spacer (ITS) MiSeq sequencing analyses were used to examine the taxonomic community structure and microbial diversity in nonrhizosphere soil (CK) and rhizosphere soils (SCC, TCC, and FCC) sampled from fields that had undergone two, three, and five years of continuous monocropping, respectively. Among the microbial communities, a decreased abundance of Acidobacteria and increased abundances of Proteobacteria and Bacteroidetes were found with the increase in monocropping years of S. flavescens. As the continuous monocropping time increased, the diversity of the bacterial community decreased, but that of fungi increased. Redundancy analysis also showed that among the properties of the rhizosphere soil, the available phosphorus, organic matter, total nitrogen, and sucrase had the greatest impacts on the diversity of the rhizosphere microbial community. Moreover, a biomarker for S. flavescens soil was also identified using the most differentially abundant bacteria and fungi in soil samples.

Conclusions

Our study indicates that long-term monocropping exerted great impacts on microbial community distributions and soil physicochemical properties. The relationship between microbial community and physicochemical properties of rhizosphere soil would help clarify the side effects of continuous S. flavescens monocropping. Our study may aid in uncovering the theoretical basis underlying obstacles to continuous monocropping and provide better guidance for crop production.

Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: Their links with microbial communities, antibiotics, and water quality

In this study, six antibiotic resistance genes (ARGs), one mobile genetic element (int1), and their relation with microbial communities, antibiotics, and water quality were investigated in and around of an agriculturally disturbed lake, namely, Lake Honghu. The ARGs and int1 in the research area had a 100 % detection frequency in each sample during two sampling times. The ARGs were higher in the rivers and inlets than in Lake Honghu. Sul1 was the main ARG in this area. Antibiotics, nutrients, and dissolved oxygen were significantly, positively, and negatively correlated with nearly all of the ARGs, respectively. This finding suggests that reducing antibiotics and the eutrophication level could reduce the risk of ARGs. Microbial community shift had the most direct contribution to ARG variation. However, when the indirect effect was considered, environmental factors contributed 34 % to the ARGs' variance, the microbial community contributed 28 %, and their joint effect contributed 27 % to the ARG profiles. The abundance of Firmicutes, Gemmatimonadetes, Proteobacteria, etc. and their positive correlation with ARGs were significant, suggesting that these phyla probably carry ARGs. The study provides a systematic profile of ARG distribution and dissemination in a typical Chinese lake and new ideas to control this emerging contaminant in lakes.