Direct observations of microbial community succession on sinking marine particles

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

[Effects of Biochar Application on Soil Bacterial Community Diversity and Winter Wheat Growth in Wheat Fields]

A long-term field experiment was conducted to study the diversity of soil bacterial communities and the response of crop growth to biochar application, in order to provide a scientific basis for the rational application of biochar in agricultural fields. Four treatments were applied at 0 (B0 blank), 5 (B1), 10 (B2), and 20 t·hm-2(B3) to investigate the effects of biochar on soil physical and chemical properties, soil bacterial community diversity, and growth of winter wheat using Illumina MiSeq high-throughput sequencing technology. The results showed that soil water content, pH value, soil organic carbon, total nitrogen, nitrate nitrogen content, winter wheat biomass, nitrogen uptake, and yield showed an increasing trend with the increase in biochar amount. The high-throughput sequencing results showed that the B2 treatment significantly reduced the alpha diversity of the bacterial community at the flowering stage. The overall response of soil bacterial community composition to different application rates of biochar and phenological phases was taxonomically consistent. In this study, Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, and Actinobacteria were the dominant bacterial phyla. The relative abundance of Acidobacteria decreased, but the relative abundance of Proteobacteria and Planctomycetes increased with biochar application. The results of redundancy analysis, co-occurrence network analysis, and PLS-PM analysis indicated that bacterial community compositions were closely associated with soil parameters such as soil nitrate and total nitrogen. The average connectivity between 16S OTUs was higher under the B2 and B3 treatments (16.966 and 14.600) than under the B0 treatment. The variation in soil bacterial community (89.1%) was regulated by biochar and sampling period and partly explained the changes in the growth dynamics of winter wheat (0.077). In conclusion, biochar application could regulate the changes in the soil bacterial community and promote crop growth after seven years of application. It is suggested that 10-20 t·hm-2 biochar should be applied in semi-arid agricultural areas to achieve sustainable agricultural development.

Impact of Insect-Resistant Transgenic Maize 2A-7 on Diversity and Dynamics of Bacterial Communities in Rhizosphere Soil

Artificial modification of Bacillus thuringiensis (Bt) proteins can effectively improve their resistance to target pests, but the effect of such modification on the diversity of rhizosphere microorganisms remains unclear. Transgenic maize 2A-7 contains two artificially modified Bt proteins, mCry1Ab and mCry2Ab. These proteins can enter soil and pose a potential threat to soil microbial diversity. To assess their impacts on rhizosphere bacteria communities, the contents of the two Bt proteins and changes in bacterial community diversity in the rhizosphere soils of transgenic maize 2A-7 and its control variety were analyzed at different growth stages in 2020. The results showed that the two Bt proteins were detected at low levels in the rhizosphere soils of 2A-7 plants. No significant differences in soil bacterial diversity were detected between 2A-7 and its control variety at any of the growth stages. Bioinformatics analysis indicated that the growth stage, rather than the cultivar, was the main factor causing changes in bacterial communities. This research provides valuable data for understanding the impact of Bt crops on the soil microbiome, and establishes a theoretical basis for evaluation of their safety.

Title: Effect of Bacillus subtilis and Lactobacillus plantarum on solid-state fermentation of soybean meal

BACKGROUD

As feeding probiotics, Bacillus subtilis FJAT-4842 and Lactobacillus plantarum FJAT-13737 were employed to improve the nutritional value and reduce the risk of contamination in the solid-state fermentation (SSF) of soybean meal (SBM).

RESULT

After fermentation with bacterium starters, the crude protein, free amino acid and lactic acid increased, with higher protease and cellulose activity. The addition of Lactobacillus plantarum could increase the crude protein and lactic acid content by 50.1% and 94.9% respectively. After fermentation, the contents of crude fiber and phytic acid decreased by 45.9% and 48.1%. Compared with control treatment, the addition of both B. subtilis FJAT-4842 and L. plantarum FJAT-13737 could effectively elevate the production of FAA and ester. Moreover, the addition of bacterium starter could prevent the production of mycotoxin. Moreover, addition of bacterium starters promoted bacterial diversity of the fermented SBM. Especially, the addition of B. subtilis could reduce the relative content of Staphylococcus. After fermentation of 7 days, lactic acid bacteria including Pediococcus, Weissella and Lactobacillus became the main bacteria in the fermented SBM.

CONCLUSION

The addition of bacterium starter is benefit to improve the nutritional value and reduce the risk of contamination in the solid state fermentation of soybean. This article is protected by copyright. All rights reserved.

Seasonal succession of microbial community co-occurrence patterns and community assembly mechanism in coal mining subsidence lakes

Coal mining subsidence lakes are classic hydrologic characteristics created by underground coal mining and represent severe anthropogenic disturbances and environmental challenges. However, the assembly mechanisms and diversity of microbial communities shaped by such environments are poorly understood yet. In this study, we explored aquatic bacterial community diversity and ecological assembly processes in subsidence lakes during winter and summer using 16S rRNA gene sequencing. We observed that clear bacterial community structure was driven by seasonality more than by habitat, and the α-diversity and functional diversity of the bacterial community in summer were significantly higher than in winter (p < 0.001). Canonical correspondence analysis indicated that temperature and chlorophyll-a were the most crucial contributing factors influencing the community season variations in subsidence lakes. Specifically, temperature and chlorophyll-a explained 18.26 and 14.69% of the community season variation, respectively. The bacterial community variation was driven by deterministic processes in winter but dominated by stochastic processes in summer. Compared to winter, the network of bacterial communities in summer exhibited a higher average degree, modularity, and keystone taxa (hubs and connectors in a network), thereby forming a highly complex and stable community structure. These results illustrate the clear season heterogeneity of bacterial communities in subsidence lakes and provide new insights into revealing the effects of seasonal succession on microbial assembly processes in coal mining subsidence lake ecosystems.

[Changes in Soil Bacterial Community Diversity in Degraded Patches of Alpine Meadow in the Source Area of the Yellow River]

MiSeq sequencing technology was used to investigate the bacterial compositions and diversities of active patch, non-active patch, recovered patch, and healthy alpine meadows so as to understand the changes in soil bacterial community diversity during altitude change and alpine meadow degradation. The relationship between bacterial diversity and environmental factors was analyzed using redundancy analysis (RDA). The results showed that the dominant bacterial phyla in the soil included Proteobacteria, Actinobacteriota, and Acidobacteriota in the study areas. The dominant bacterial genera that were identified via the MiSeq were RB41, Sphingomonas, and Bradyrhizobium. The relative abundance of these genera decreased with altitude increase and increased with the restoration progress of degraded patches but was significantly lower than that in the alpine meadow (P<0.05). The abundance of functional bacteria related to carbon fixation in degraded patches was higher than that in the healthy alpine meadow. The bacterial Chao1 index and species number in different types of degraded patches were significantly higher than those in the alpine meadow (P<0.05). The results of the RDA suggest that biological soil crust coverage and total nitrogen were the main influencing factors on dominant bacterial phyla at the altitude of 4013 m. Biomass, total nitrogen, and pH had a great influence on the dominant bacterial phyla at the altitude of 4224 m. Biomass and total potassium significantly affected the distribution of bacterial genera at the altitude of 4013 m. Sedge coverage and available nitrogen were the main influencing factors on bacterial dominant genera at the altitude of 4224 m. Biological soil crusts and pH had a great influence on bacterial diversities. The bacterial influence factors varied greatly at different altitude areas. Therefore, we should not only pay attention to the effect of alpine meadow degradation but also consider the effect of altitude in the study of bacterial diversity changes.

Comparative Analyses of Rhizosphere Bacteria Along an Elevational Gradient of Thuja sutchuenensis

Thuja sutchuenensis Franch. is an endangered species in southwestern China, primarily distributed in 800-2,100 m of inaccessible mountainous areas. Rhizosphere soil physicochemical properties and bacterial communities play an essential role in managing plant growth and survival. Nonetheless, the study investigating rhizosphere soil properties and bacterial communities of T. sutchuenensis is limited. The present study investigated soil properties, including soil pH, organic matter, water content, nitrogen, phosphorus, and potassium contents, and bacterial communities in nearly all extant T. sutchuenensis populations at five elevational gradients. Our results demonstrated that the increase in elevation decreased rhizosphere and bulk soil phosphorus content but increased potassium content. In addition, the elevational gradient was the dominant driver for the community composition differentiation of soil bacterial community. Proteobacteria and Acidobacteria were the dominant bacterial phyla distributed in the rhizosphere and bulk soils. Co-occurrence network analysis identified key genera, including Bradyrhizobium, Acidicapsa, Catenulispora, and Singulisphaera, that displayed densely connected interactions with many genera in the rhizosphere soil. The dominant KEGG functional pathways of the rhizosphere bacteria included ABC transporters, butanoate metabolism, and methane metabolism. Further correlation analysis found that soil phosphorus and potassium were the dominant drivers for the diversity of soil bacteria, which were distinctively contributed to the phylum of Planctomycetes and the genera of Blastopirellula, Planctomycetes, and Singulisphaera. Collectively, this comprehensive study generated multi-dimensional perspectives for understanding the soil bacterial community structures of T. sutchuenensis, and provided valuable findings for species conservation at large-scale views.

Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut (Arachis hypogaea L.) Cultivars

Background: Exposure of seeds to high salinity can cause reduced germination and poor seedling establishment. Improving the salt tolerance of peanut (Arachis hypogaea L.) seeds during germination is an important breeding goal of the peanut industry. Bacterial communities in the spermosphere soils may be of special importance to seed germination under salt stress, whereas extant results in oilseed crop peanut are scarce. Methods: Here, bacterial communities colonizing peanut seeds with salt stress were characterized using 16S rRNA gene sequencing. Results: Peanut spermosphere was composed of four dominant genera: Bacillus, Massilia, Pseudarthrobacter, and Sphingomonas. Comparisons of bacterial community structure revealed that the beneficial bacteria (Bacillus), which can produce specific phosphatases to sequentially mineralize organic phosphorus into inorganic phosphorus, occurred in relatively higher abundance in salt-treated spermosphere soils. Further soil enzyme activity assays showed that phosphatase activity increased in salt-treated spermosphere soils, which may be associated with the shift of Bacillus. Conclusion: This study will form the foundation for future improvement of salt tolerance of peanuts at the seed germination stage via modification of the soil microbes.

Symbiotic skin bacteria as a source for sex-specific scents in frogs

Amphibians are known to possess a wide variety of compounds stored in their skin glands. While significant progress has been made in understanding the chemical diversity and biological relevance of alkaloids, amines, steroids, and peptides, most aspects of the odorous secretions are completely unknown. In this study, we examined sexual variations in the volatile profile from the skin of the tree frog Boana prasina and combined culture and culture-independent methods to investigate if microorganisms might be a source of these compounds. We found that sesquiterpenes, thioethers, and methoxypyrazines are major contributors to the observed sex differences. We also observed that each sex has a distinct profile of methoxypyrazines, and that the chemical origin of these compounds can be traced to a Pseudomonas sp. strain isolated from the frog's skin. This symbiotic bacterium was present in almost all individuals examined from different sites and was maintained in captive conditions, supporting its significance as the source of methoxypyrazines in these frogs. Our results highlight the potential relevance of bacteria as a source of chemical signals in amphibians and contribute to increasing our understanding of the role that symbiotic associations have in animals.

Biogeographical distribution of bacterial communities in Changbai Mountain, Northeast China

The broad-leaved and Korean pine mixed forest in Changbai Mountain, China is an important component of boreal forest; the area is sensitive to global climate change. To understand spatial distribution patterns of soil bacterial community along elevation, we analyzed the soil bacterial community diversity and composition along an elevational gradient of 699-1177 m in a primitive Korean pine forest in Changbai Mountain using the high-throughput sequencing. In total, 149,519 optimized sequences were obtained. Bacterial Shannon index increased along elevation from 699 m to 937 m and started to decrease at the elevation of 1,044 m, showing a humpback curve along elevation. Evenness (ACE index) and richness (Chao index) of the soil bacterial community both decreased with elevation (the highest values of 770 and 762 at 699 m and the lowest values of 548 and 539 at 1,177 m, respectively), all the indices are significantly different between elevations. Bacterial composition at phylum and genus levels had some differences between elevations, but the dominant bacterial populations were generally consistent. Beta-diversity analysis showed a distance-decay pattern of bacterial community similarity at different samples. Soil physical and chemical properties explained 70.78% of the variation in bacterial community structure (soil pH explained 19.95%), and elevational distance only explained 8.42%. In conclusion, the contemporary environmental disturbances are the critical factors in maintaining the bacterial spatial distribution compared with historical contingencies.

Effects of inoculation with organic-phosphorus-mineralizing bacteria on soybean (Glycine max) growth and indigenous bacterial community diversity

Three different organic-phosphorus-mineralizing bacteria (OPMB) strains were inoculated to soil planted with soybean (Glycine max), and their effects on soybean growth and indigenous bacterial community diversity were investigated. Inoculation with Pseudomonas fluorescens Z4-1 and Brevibacillus agri L7-1 increased organic phosphorus degradation by 22% and 30%, respectively, compared with the control at the mature stage. Strains P. fluorescens Z4-1 and B. agri L7-1 significantly improved the soil alkaline phosphatase activity, average well color development, and the soybean root activity. Terminal restriction fragment length polymorphism analysis demonstrated that P. fluorescens Z4-1 and B. agri L7-1 could persist in the soil at relative abundances of 2.0%-6.4% throughout soybean growth. Thus, P. fluorescens Z4-1 and B. agri L7-1 could potentially be used in organic-phosphorus-mineralizing biofertilizers. OPMB inoculation altered the genetic structure of the soil bacterial communities but had no apparent influence on the carbon source utilization profiles of the soil bacterial communities. Principal components analysis showed that the changes in the carbon source utilization profiles of bacterial community depended mainly on the plant growth stages rather than inoculation with OPMB. The results help to understand the evolution of the soil bacterial community after OPMB inoculation.

[Comparative Analysis of the Bacterial Community on Anodic Biofilms in Sediment Microbial Fuel Cell Under Open and Closed Circuits]

To investigate the differences in microbial community of anodic biofilms under open and closed circuits, sediment microbial fuel cell (SMFCs) reactors connecting with a 5 kΩ external resistance and open circuit during the start-up period were operated individually. Anodic biofilms were collected and analyzed using Solexa high-throughput sequencing technology. A total of 3936 and 3930 operational taxonomic units (OTUs) were obtained from the anodic biofilms under open and closed circuits, respectively. After 97% similarity merging, 1581 and 1551 OTUs were finally determined from open and close circuit biofilms, respectively. The analysis of α diversity showed that bacterial diversity of anodic biofilm under open circuit was higher than that under closed circuit. The dominant bacterial were Proteobacteria, Firmicutes and Bacteroidetes for both open and closed circuits. They accounted for 59.79%, 12.54% and 9.02% under open circuit biofilm respectively; and these values were 63.02%, 10.01% and 3.60% in the closed circuit biofilm respectively, and Geobacter accounted for 16.55% in the closed circuit biofilm. The present study demonstrated that the electron transfer process during start-up period affected the microbial community structure of the anodic biofilms.