Bacterial community structure of Physalis peruviana L. fruit exocarp and the presence of pathogens with possible implications on food safety.

Introduction: Cape gooseberry (Physalis peruviana L.) is a wellconsumed crop in Ecuador, whose fruits are abundant in bioactive molecules. Its rapid post-harvest deterioration and safety limit its market potential. Methodology: To gather baseline data on the prevalence of bacterial taxa among groups, we employed 16S ribosomal RNA (16S rRNA) amplicon gene sequencing to detect changes in the bacterial community structure in cape gooseberry fruits harvested from an organic farm production system (# 270 samples x two ripeness stages), and fruits obtained from an open-air market (#270). Results: This is the first report of bacterial taxa inhabiting cape gooseberry fruits. Shannon's diversity index revealed that the fruits purchased from the market and the unripe stage had the highest level of bacterial diversity (average Shannon indices of 3.3 and 3.1) followed by those collected from the field at the mature ripe stage (2.07). Alpha diversity analysis indicated that there were no significant differences in the number of taxa or evenness within the sample, whereas there was a significant difference in beta diversity between the groups. Rhizobiaceae was the most abundant family in fruits originating from the field regardless of the ripe stage, while Acetobacteraceae, Pseudomonadaceae, Fusobacteriaceae, Bacteroidaceae, and Erwiniaceae were the most abundant families in the market group. At the genus level, Liberibacter was the most abundant phytopathogen in fruits originating from the field, while Gluconobacter was the most abundant in samples collected from the market. The phytopathogen Candidatus_Liberibacter was the most abundant in samples collected from the field, while the fruits purchased from the market stands contained opportunistic enteric pathogens such as Escherichia vulneris, Klebsiella pneumoniae, and K. variicola, their relative abundance varied with the sample. In addition, potential pathogens of animal origin such as Fusobacterium necrophorum, Porphyromonas levii, Helcococcus ovis, and Trueperella pyogenes were found in almost all samples at varying relative abundance. Conclusion: Our study provides basic information on the microbiome of cape gooseberries from agriculture fields to the table along with the detection of several pathogenic microorganisms with possible impact on food safety and public health therefore, strategies for reducing bacterial contamination in both farm and retail markets are compulsory.

Native and non-native freshwater bivalves in the bioremediation of bacterial pollution caused by the disposal of sewage.

Treated sewage contains a large diversity of pathogens that can be transmitted to the environment and, directly or indirectly, infect humans through water use (i.e., consumption, bathing, or irrigation). In urban environments, wastewater normally flows into wastewater treatment plants (WWTPs), where it is subjected to different processes in order to eliminate the greatest amount of waste. However, there are inequalities among European countries concerning wastewater management. In this context, we evaluate the potential of freshwater mussels to improve water quality (i.e., reduce bacterial abundance) in rivers receiving primary, secondary, or tertiary sewage-treated effluents. Additionally, because freshwater mussels are declining at a global scale and empty niches are progressively occupied by non-native counterparts, we evaluate if depauperate communities and the Asian clams, Corbicula genus, can provide equivalent ecosystem services (i.e., water quality improvement by biofiltration) formerly provided by diverse native communities. For this, an analysis of the bacterial biodiversity of the samples filtered by the different bivalve communities was carried out. The experimental approach was performed by metabarcoding the 16S rRNA gene using Illumina technologies. According to the results obtained, secondary treatment processes were effective in reducing the bacterial diversity. Furthermore, the waters filtered by the bivalves presented a lower bacterial abundance for certain genera. Biofiltration differs, however, among species, with Corbicula reducing a large number of taxa much more efficiently than native freshwater mussels in both diverse and depauperated communities. These results are likely related to Corbicula being a generalist species in front of native mussels, which may be more selective. Considering it is not possible to eradicate Corbicula from European rivers, its filtering capacity should be considered when managing freshwater ecosystems.

Deciphering the geochemical influences on bacterial diversity and communities among two Algerian hot springs.

Northeastern Algeria boasts numerous hot springs, yet these hydrothermal sites remain largely unexplored for their microbial ecology. The present study explores the bacterial abundance and diversity within two distinct Algerian hot springs (Hammam Saïda and Hammam Debagh) and investigates the link between the prevailing bacteria with geochemical parameters. High-throughput 16S rRNA gene sequencing of water and sediment samples revealed a bacterial dominance of 99.85-91.16% compared to Archaea (0.14-0.66%) in both springs. Interestingly, Saïda hot spring, characterized by higher temperatures and sodium content, harbored a community dominated by Pseudomonadota (51.13%), whereas Debagh, a Ca-Cl-SO4 type spring, was primarily populated by Bacillota with 55.33%. Bacteroidota displayed even distribution across both sites. Additional phyla, including Chloroflexota, Deinococcota, Cyanobacteriota, and Chlorobiota, were also present. Environmental factors, particularly temperature, sodium, potassium, and alkalinity, significantly influenced bacterial diversity and composition. These findings shed light on the interplay between distinct microbial communities and their associated geochemical properties, providing valuable insights for future research on biogeochemical processes in these unique ecosystems driven by distinct environmental conditions, including potential applications in bioremediation and enzyme discovery.

Corrigendum: Human gut microbiome across different lifestyles: from hunter-gatherers to urban populations.

[This corrects the article DOI: 10.3389/fmicb.2022.843170.].

[Effects of Different Microbial Fertilizers on Soil Quality and Maize Yield in Coastal Saline Soil].

Microbial fertilizers have the characteristics of high efficiency and environmental protection in improving saline soils, and the application of functional microbial fertilizers is of great significance for the green abatement of saline barriers and the improvement of soil quality in coastal areas. The experiment was based on moderately saline soil in the coastal area of Hebei Province, with corn as the indicator crop, on the basis of conventional chemical fertilizer application. Different microbial fertilizer treatments, namely, T1 （conventional chemical fertilizer 750 kg·hm-2 + compound microbial agent 75 kg·hm-2）, T2 （conventional chemical fertilizer 750 kg·hm-2 + Bacillus megaterium 300 kg·hm-2）, T3 （conventional chemical fertilizer 750 kg·hm-2 + B. mucilaginosus 300 kg·hm-2）, T4 （conventional chemical fertilizer 750 kg·hm-2 + organic silicon fertilizer 600 kg·hm-2）, T5 （conventional chemical fertilizer 750 kg·hm-2 + bio-organic fertilizer 600 kg·hm-2）, T6 （conventional fertilizer 750 kg·hm-2 + active microalgae 15 kg·hm-2）, and CK （only fertilizer 750 kg·hm-2）, were used for these seven treatments, to study the effects of different microbial fertilizers on soil nutrients, salinity, bacterial community, and corn yield and economic efficiency during two critical periods （V12 stage and maturity stage） of corn. The results showed that compared with that in CK, T1 significantly increased soil total nitrogen （TN） and available phosphorus （AP） contents during the whole growth period. Over the whole reproductive period, soil organic matter （OM） at maturity increased by 10.35% over the V12 stage compared to that in CK, but there was no significant difference between treatments. Compared with that in CK, T5 and T6 significantly reduced soil total salinity and Ca2+ content during the whole growth period by an average of 14.51%-18.48% and 24.25%-25.51%. T1 significantly increased the bacterial diversity index over the whole growth period by 45.16% compared to that in CK. The dominant soil phyla were Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, and the dominant genera were Bacillus and Geminicoccaceae. The most abundant functions of the bacterial community in the study area were chemoheterotrophy and aerobic chemoheterotrophy, with average relative abundances of 28.89% and 27.11%, and T3 and T6 significantly improved soil N cycling function. The results of redundancy analysis （RDA） indicated that Na+, SO42-, pH, and EC were important factors driving the structure of the bacterial community, and correlation heatmaps showed that Na+, SO42-, pH, and EC were significantly and positively correlated mainly with the phylum Planctomycetota, whereas soil OM and TN were significantly and positively correlated with Cyanobacteria. Compared with that in CK, T6 increased the relative abundance of Cyanobacteria and optimized the bacterial community structure during the whole growth period. Using recommended dosages of bacterial fertilizers T1 and T6 increased maize yield by 7.31%-24.83% and economic efficiency by 9.05%-23.23%, respectively. The preliminary results of soil chemical properties and yield correlation analysis revealed that EC, AP, HCO3-, and Mg2+ were the obstacle factors limiting soil productivity in coastal areas. In conclusion, the use of the compound bacterial agent （T1） and active microalgae （T6） at the recommended dosage can significantly enhance soil nutrients, reduce salinity, and improve the structural diversity of soil bacterial communities, which not only ensures the increase in maize yield and efficiency but also realizes the efficient use of microbial fertilizers and the improvement of soil quality.

Temporal changes in the morphological and microbial diversity of biofilms on the surface of a submerged stone in the Danube River.

Epilithic biofilms are ubiquitous in large river environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, the seasonal succession in the morphological structure and the taxonomic composition of an epilithic bacterial biofilm community at a polluted site of the Danube River were followed using electron microscopy, high-throughput 16S rRNA gene amplicon sequencing and multiplex/taxon-specific PCRs. The biofilm samples were collected from the same submerged stone and carried out bimonthly in the littoral zone of the Danube River, downstream of a large urban area. Scanning electron microscopy showed that the biofilm was composed of diatoms and a variety of bacteria with different morphologies. Based on amplicon sequencing, the bacterial communities were dominated by the phyla Pseudomonadota and Bacteroidota, while the most abundant archaea belonged to the phyla Nitrososphaerota and Nanoarchaeota. The changing environmental factors had an effect on the composition of the epilithic microbial community. Critical levels of faecal pollution in the water were associated with increased relative abundance of Sphaerotilus, a typical indicator of "sewage fungus", but the composition and diversity of the epilithic biofilms were also influenced by several other environmental factors such as temperature, water discharge and total suspended solids (TSS). The specific PCRs showed opportunistic pathogenic bacteria (e.g. Pseudomonas spp., Legionella spp., P. aeruginosa, L. pneumophila, Stenotrophomonas maltophilia) in some biofilm samples, but extended spectrum ß-lactamase (ESBL) genes and macrolide resistance genes could not be detected.

Substantially altered bacterial diversity associated with developmental stages of litchi stink bug, Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae).

The mutualistic symbiotic relationship between insects and bacteria greatly influences the growth and development of host insects. Tessaratoma javanica (Thunberg) (Hemiptera: Tessaratomidae), also referred to as the litchi stink bug, has recently been established as an important insect pest of Litchi chinensis Sonn. and causes substantial yield loss in India. To design effective and environmentally safe management strategies, an understanding of the diversity and functions of microbiota harbored across the development stages is very important. The assessment of the diversity of development-associated bacteria in T. javanica and their predicted functions was conducted using 16S rRNA gene sequences obtained by the Illumina MiSeq technology. The result showed that taxonomic analysis of associated bacteria in different developmental stages includes a total of 46 phyla, encompassing 139 classes, 271 orders, 474 families, and 893 genera of bacteria. All developmental stages of T. javanica shared a total of 42.82 percent of operational taxonomic units (OTUs), with a 97 % similarity threshold. Alpha diversity indices showed maximum species richness in the egg and adult stages. The phyla Proteobacteria followed by Firmicutes, Bacteriodetes, and Actinobacteria, exhibited the highest levels of abundance across all the developmental stages of T. javanica. Microbiota were most different between the egg and the 4th nymphal stage (χ2 = 711.67) and least different between the 2nd and 4th nymphal instars (χ2 = 44.45). The predicted functions of the microbiota associated with T. javanica are mainly involved in amino acid metabolism, cell motility, cellular processes and signaling, glycan biosynthesis and metabolism, lipid metabolism, and membrane transport. The present study documentation and information on symbiotic bacteria across T. javanica life stages will prompt the development of novel biological management strategies.

An optimal combined slow-release nitrogen fertilizer and urea can enhance the decomposition rate of straw and the yield of maize by improving soil bacterial community and structure under full straw returning system.

Under a full straw returning system, the relationship between soil bacterial community diversity and straw decomposition, yield, and the combined application of slow-release nitrogen and urea remains unclear. To evaluate these effects and provide an effective strategy for sustainable agricultural production, a 2-year field positioning trial was conducted using maize as the research object. Six experimental treatments were set up: straw returning + no nitrogen fertilizer (S1N0), straw returning + slow-release nitrogen fertilizer:urea = 0:100% (S1N1), straw returning + slow-release nitrogen fertilizer:urea = 30%:70% (S1N2), straw returning + slow-release nitrogen fertilizer:urea = 60%:40% (S1N3), straw returning + slow-release nitrogen fertilizer:urea = 90%:10% (S1N4), and straw removal + slow-release nitrogen fertilizer:urea = 30%:70% (S0N2). Significant differences (p < 0.05) were observed between treatments for Proteobacteria, Acidobacteriota, Myxococcota, and Actinobacteriota at the jointing stage; Proteobacteria, Acidobacteriota, Myxococcota, Bacteroidota, and Gemmatimonadota at the tasseling stage; and Bacteroidota, Firmicutes, Myxococcota, Methylomirabilota, and Proteobacteria at the maturity stage. The alpha diversity analysis of the soil bacterial community showed that the number of operational taxonomic units (OTUs) and the Chao1 index were higher in S1N2, S1N3, and S1N4 compared with S0N2 at each growth stage. Additionally, the alpha diversity measures were higher in S1N3 and S1N4 compared with S1N2. The beta diversity analysis of the soil bacterial community showed that the bacterial communities in S1N3 and S1N4 were more similar or closely clustered together, while S0N2 was further from all treatments across the three growth stages. The cumulative straw decomposition rate was tested for each treatment, and data showed that S1N3 (90.58%) had the highest decomposition rate. At the phylum level, straw decomposition was positively correlated with Proteobacteria, Actinobacteriota, Myxococcota, and Bacteroidota but significantly negatively correlated with Acidobacteriota. PICRUSt2 function prediction results show that the relative abundance of bacteria in soil samples from each treatment differed significantly. The maize yield of S1N3 was 15597.85 ± 1477.17 kg/hm2, which was 12.80 and 4.18% higher than that of S1N1 and S0N2, respectively. In conclusion, a combination of slow-release nitrogen fertilizer and urea can enhance the straw decomposition rate and maize yield by improving the soil bacterial community and structure within a full straw returning system.

Multiple cropping effectively increases soil bacterial diversity, community abundance and soil fertility of paddy fields.

BACKGROUND: Crop diversification is considered as an imperative approach for synchronizing the plant nutrient demands and soil nutrient availability. Taking two or more crops from the same field in one year is considered as multiple cropping. It improves the diversity and abundance of soil microbes, thereby improving the growth and yield of crops. Therefore, the present study was conducted to explore the effects of different multiple winter cropping on soil microbial communities in paddy fields. In this study, eight rice cropping patterns from two multiple cropping systems with three different winter crops, including Chinese milk vetch (CMV), rape, and wheat were selected. The effects of different multiple winter cropping on soil microbial abundance, community structure, and diversity in paddy fields were studied by 16 S rRNA high-throughput sequencing and real-time fluorescence quantitative polymerase chain reaction (PCR). RESULTS: The results showed that different multiple winter cropping increased the operational taxonomic units (OTUs), species richness, and community richness index of the bacterial community in 0 ~ 20 cm soil layer. Moreover, soil physical and chemical properties of different multiple cropping patterns also affected the diversity and abundance of microbial bacterial communities. The multiple cropping increased soil potassium and nitrogen content, which significantly affected the diversity and abundance of bacterial communities, and it also increased the overall paddy yield. Moreover, different winter cropping changed the population distribution of microorganisms, and Proteobacteria, Acidobacteria, Nitrospira, and Chloroflexi were identified as the most dominant groups. Multiple winter cropping, especially rape-early rice-late rice (TR) andChinese milk vetch- early rice-late rice (TC) enhanced the abundance of Proteobacteria, Acidobacteria, and Actinobacteria and decreased the relative abundance of Verrucomicrobia and Euryarchaeota. CONCLUSION: In conclusion, winter cropping of Chinese milk vetch and rape were beneficial to improve the soil fertility, bacteria diversity, abundance and rice yield.

Reducing Application of Nitrogen Fertilizer Increases Soil Bacterial Diversity and Drives Co-Occurrence Networks.

Reducing nitrogen fertilizer application highlights its role in optimizing soil bacterial communities to achieve sustainable agriculture. However, the specific mechanisms of bacterial community change under these conditions are not yet clear. In this study, we employed long-term field experiments and high-throughput sequencing to analyze how varying levels of nitrogen application influence the soil bacterial community structure and co-occurrence networks. The results show that reducing the nitrogen inputs significantly enhances the diversity and evenness of the soil bacterial communities, possibly due to the diminished dominance of nitrogen-sensitive taxa, which in turn liberates the ecological niches for less competitive species. Furthermore, changes in the complexity and stability of the bacterial co-occurrence networks suggest increased community resilience and a shift toward more mutualistic interactions. These findings underline the potential of reduced nitrogen application to alleviate competitive pressures among bacterial species, thereby promoting a more diverse and stable microbial ecosystem, highlighting the role of competitive release in fostering microbial diversity. This research contributes to our understanding of how nitrogen management can influence soil health and offers insights into sustainable agricultural practices.

Long-Term Contaminant Exposure Alters Functional Potential and Species Composition of Soil Bacterial Communities in Gulf Coast Prairies.

Environmental pollution is a persistent threat to coastal ecosystems worldwide, adversely affecting soil microbiota. Soil microbial communities perform critical functions in many coastal processes, yet they are increasingly subject to oil and heavy metal pollution. Here, we assessed how small-scale contamination by oil and heavy metal impacts the diversity and functional potential of native soil bacterial communities in the gulf coast prairie dunes of a barrier island in South Texas along the northern Gulf of Mexico. We analyzed the bacterial community structure and their predicted functional profiles according to contaminant history and examined linkages between species diversity and functional potential. Overall, contaminants altered bacterial community compositions without affecting richness, leading to strongly distinct bacterial communities that were accompanied by shifts in functional potential, i.e., changes in predicted metabolic pathways across oiled, metal, and uncontaminated environments. We also observed that exposure to different contaminants can either lead to strengthened or decoupled linkages between species diversity and functional potential. Taken together, these findings indicate that bacterial communities might recover their diversity levels after contaminant exposure, but with consequent shifts in community composition and function. Furthermore, the trajectory of bacterial communities can depend on the nature or type of disturbance.

Changes in soil bacterial community characteristics in patches of different vegetation types under different stages of restoration in the desert of northern China.

In desert areas, the process of mobile sandy land changing to semi-fixed sandy land and eventually to fixed sandy land after undergoing vegetation restoration is inevitable. The presence of shrub patches and herb patches is common in this restoration process. No relevant studies have reported the soil bacterial community characteristics of different vegetation-type patches (shrub patches and herb patches) under different stages of restoration. Therefore, we utilized long-established experimental plots to collect soil from 0-20 cm soil layer under shrub patches (dominated by Salix psammophila) and herb patches under different stages of restoration (i.e., mobile sand land, semi-fixed sand land, and fixed sand land), by determining soil physicochemical properties, enzyme activities, and soil bacterial communities. Our results found that soil bacterial α-diversity under different restoration stages showed higher shrub patches than herb patches. The dominant bacterial communities (phyla) in shrub patches and herb patches at different recovery stages were Actinobacteria, Proteobacteria, and Bacteroidota. When the mobile sandy land returned to fixed sandy land, the relative abundance of Actinobacteria and Bacteroidota gradually decreased under shrub patches and herb patches, while the relative abundance of Proteobacteria increased significantly. In addition, herb patches significantly increased the relative abundance of bacteria (genus) relative to shrub patches at different stages of recovery. Soil nutrients, soil fine particles, and soil enzyme activities were significantly higher under shrub patches than under herb patches when fixed sandy land due to differences in life form and architecture between shrub patches and herb patches. Based on this, soil bacterial community composition and diversity under shrub patches were driven by more soil properties during the restoration of sandy land. This study complements the dynamic recovery processes and driving mechanisms of soil bacterial community structure under different vegetation patches in sandy areas, especially in the context of global climate change.

Beyond the Bloom: Unraveling the Diversity, Overlap, and Stability of Free-Living and Particle-Attached Bacterial Communities in a Cyanobacteria-Dominated Hypereutrophic Lake.

In aquatic ecosystems with low nutrient levels, organic aggregates (OAs) act as nutrient hotspots, hosting a diverse range of microbial species compared to those in the water column. Lake eutrophication, marked by intensified and prolonged cyanobacterial blooms, significantly impacts material and energy cycling processes, potentially altering the ecological traits of both free-living (FL) and particle-attached (PA) bacteria. However, the extent to which observed patterns of FL and PA bacterial diversity, community assembly, and stability extend to hypereutrophic lakes remains understudied. To address this gap, we investigated bacterial diversity, composition, assembly processes, and stability within hypereutrophic Lake Xingyun. Our results revealed that FL bacterial communities exhibited higher α-diversity than PA counterparts, coupled with discernible taxonomic compositions. Both bacterial communities showed distinct seasonality, influenced by cyanobacterial bloom intensity. Environmental factors accounted for 71.1% and 54.2% of the variation among FL and PA bacteria, respectively. The assembly of the PA bacterial community was predominantly stochastic, while FL assembly was more deterministic. The FL network demonstrated greater stability, complexity, and negative interactions, indicative of competitive relationships, while the PA network showed a prevalence of positive correlations, suggesting mutualistic interactions. Importantly, these findings differ from observations in oligotrophic, mesotrophic, and eutrophic lakes. Overall, this research provides valuable insights into the interplay among bacterial fractions, enhancing our understanding of nutrient status and cyanobacterial blooms in shaping bacterial communities.

Soil bacterial communities affected by land-use types in a small catchment area of the Balaton Uplands (Hungary).

Changes resulting from different tillage practices can affect the structure of microbial communities, thereby altering soil ecosystems and their functioning. The aim of this study was to explore and compare the physical, chemical properties and bacterial community composition of soils from different land use types (forest, grassland, vineyard, and arable field) in a small catchment. 16S rRNA gene-based amplicon sequencing was used to reveal the taxonomic diversity of summer and autumn soil samples taken from two different slope positions. The greater the anthropogenic impact was on the type of land use, the greater the change was in soil physical and chemical parameters. All sample types were dominated by the phyla Pseudomonadota, Acidobacteriota, Actinobacteriota, Bacteroidota and Verrucomicrobiota. Differences in the relative abundance of various bacterial taxa reflected the different land use types, the seasonality, and the topography. These diversity changes were consistent with the differences in soil properties.

Changes in the taxonomic composition of soil bacterial communities under different inter-row tillage managements in a sloping vineyard of the Balaton Uplands (Hungary).

The common grape (Vitis vinifera L.) has been cultivated for thousands of years. Nowadays, it is cultivated using a variety of tillage practices that affect the structure of the soil microbial communities and thus the health of the vine. The aim of this study was to explore and compare the effects of tillage (shallow tillage with bare soil) and no-tillage (perennial grass cover) practices on soil physical and chemical properties and soil bacterial community diversities in a small catchment. Soil samples were taken in July and October 2020 at different slope positions of two vineyards exposed to erosion. The two sampling sites were separated by the agricultural inter-row management type: tilled and no-tilled slopes. The taxonomic diversity of bacterial communities was determined using 16S rRNA gene-based amplicon sequencing method on Illumina MiSeq platform. Based on the examined soil properties, the sampling areas were separated from each other according to the positions of the upper and lower slopes and the sampling times. Both the tilled and no-tilled soil samples were dominated by sequences assigned to phyla Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Gemmatimonadota. The results showed that tillage had no significant effect compared to the no-tilled samples in the studied area. Water runoff and seasonally changed soil physical and chemical properties affected mainly the bacterial community structures.

[Altitude Distribution Characteristics of Farmland Soil Bacteria in Loess Hilly Region of Ningxia].

It is of great significance for the conservation of biodiversity in farmland ecosystems to study the diversity, structure, functions, and biogeographical distribution of soil microbes in farmland and their influencing factors. High-throughput sequencing technology was used to analyze the distribution characteristics of soil bacterial diversity, community structure, and metabolic function along elevation and their responses to soil physicochemical properties in farmland in the loess hilly areas of Ningxia. The results showed that:① The Alpha diversity index of soil bacterial was significantly negatively correlated with elevation (P < 0.05) and showed a trend of decreasing and then slightly increasing along the elevation. ② Seven phyla, including Proteobacteria, Actinobacteria, and Acidobacteria, were the dominant groups, and five of them showed highly significant differences between altitudes (P < 0.01). ③ At the secondary classification level, there were 36 metabolic functions of bacteria, including membrane transport, carbohydrate metabolism, and amino acid metabolism, of which 22 showed significant differences, and 12 showed extremely significant differences among different altitudes. ④ Pearson correlation analysis showed that soil water content, bulk density, pH, and carbon-nitrogen ratio had the most significant effects on bacterial Alpha diversity, whereas soil nutrients such as total organic carbon, total nitrogen, and total phosphorus had significant effects on bacterial Beta diversity. ⑤ Mantel test analysis showed that the soil water content, total organic carbon, and carbon-nitrogen ratio affected bacterial community structure at the phylum level, and soil pH, total organic carbon, total nitrogen, total phosphorus, and carbon-nitrogen ratio were significantly correlated with bacterial metabolic function. Variance partitioning analysis showed that soil water content had the highest explanation for the community structure of soil bacteria, whereas soil pH had the highest explanation for metabolic function. In conclusion, soil water content and pH were the main factors affecting the diversity, community composition, and metabolic function of soil bacteria in farmland in the loess hilly region of Ningxia.

The gut bacterial composition across life stages of Sarcophaga peregrina (Diptera: Sarcophagidae) and the effects of amikacin on their development.

Insects and microorganisms, ubiquitous organisms in the natural world, have developed intricate relationships throughout their evolutionary histories. However, most studies have concentrated on specific time points or life stages, but some limited studies have investigated the dynamics of microbial diversity within insects across life stages. Here, 16S rDNA sequencing technology was used to investigate the gut bacterial community across the life stages of Sarcophaga peregrina (Robineau-Desvoidy) (Diptera: Sarcophagidae). The results revealed that the gut bacterial diversity of S. peregrina varied with life stage and showed similarity in the nearby life stages. Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in S. peregrina. Genera such as Providencia, Ignatzschineria, and Myroides are implicated in potentially pivotal roles during the developmental processes of this flesh fly. Furthermore, the effects of amikacin on the growth and development of S. peregrina were not statistically significant. However, we did observe significant changes at the protein level, which suggests a close association between protein-level alterations and growth and development. Additionally, we speculate that S. peregrina regulates its nutritional status during nonfeeding stages to meet the demands of eclosion. This study represents the first comprehensive examination of the intestinal bacterial composition across various life stages of S. peregrina. Our findings deepen our understanding of the gut microbiota in this flesh fly and lay the groundwork for further exploration into the intricate interactions between microorganisms and insects.

Elucidating the structure, and composition of bacterial symbionts in the gut regions of wood-feeding termite, Coptotermes formosanus and their functional profile towards lignocellulolytic systems.

The wood-feeding termite, Coptotermes formosanus, presents an efficient lignocellulolytic system, offering a distinctive model for the exploration of host-microbial symbiosis towards lignocellulose degradation. Despite decades of investigation, understanding the diversity, community structure, and functional profiles of bacterial symbionts within specific gut regions, particularly the foregut and midgut of C. formosanus, remains largely elusive. In light of this knowledge gap, our efforts focused on elucidating the diversity, community composition and functions of symbiotic bacteria inhabiting the foregut, midgut, and hindgut of C. formosanus via metagenomics. The termite harbored a diverse community of bacterial symbionts encompassing 352 genera and 26 known phyla, exhibiting an uneven distribution across gut regions. Notably, the hindgut displayed a higher relative abundance of phyla such as Bacteroidetes (56.9%) and Spirochetes (23.3%). In contrast, the foregut and midgut were predominantly occupied by Proteobacteria (28.9%) and Firmicutes (21.2%) after Bacteroidetes. The foregut harbored unique phyla like Candidate phylum_TM6 and Armatimonadetes. At the family level, Porphyromonadaceae (28.1, 40.6, and 53.5% abundance in foregut, midgut, and hindgut, respectively) and Spirochaetaceae (foregut = 9%, midgut = 16%, hindgut = 21.6%) emerged as dominant families in the termite's gut regions. Enriched operational taxonomic units (OTUs) were most abundant in the foregut (28), followed by the hindgut (14), while the midgut exhibited enrichment of only two OTUs. Furthermore, the functional analyses revealed distinct influences of bacterial symbionts on various metabolic pathways, particularly carbohydrate and energy metabolisms of the host. Overall, these results underscore significant variations in the structure of the bacterial community among different gut regions of C. formosanus, suggesting unique functional roles of specific bacteria, thereby inspiring further investigations to resolve the crosstalk between host and microbiomes in individual gut-regions of the termite.

Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coral Acropora pulchra.

Background: Rainfall-induced coastal runoff represents an important environmental impact in near-shore coral reefs that may affect coral-associated bacterial microbiomes. Shifts in microbiome community composition and function can stress corals and ultimately cause mortality and reef declines. Impacts of environmental stress may be site specific and differ between coral microbiome compartments (e.g., tissue versus mucus). Coastal runoff and associated water pollution represent a major stressor for near-shore reef-ecosystems in Guam, Micronesia. Methods: Acropora pulchra colonies growing on the West Hagåtña reef flat in Guam were sampled over a period of 8 months spanning the 2021 wet and dry seasons. To examine bacterial microbiome diversity and composition, samples of A. pulchra tissue and mucus were collected during late April, early July, late September, and at the end of December. Samples were collected from populations in two different habitat zones, near the reef crest (farshore) and close to shore (nearshore). Seawater samples were collected during the same time period to evaluate microbiome dynamics of the waters surrounding coral colonies. Tissue, mucus, and seawater microbiomes were characterized using 16S DNA metabarcoding in conjunction with Illumina sequencing. In addition, water samples were collected to determine fecal indicator bacteria (FIB) concentrations as an indicator of water pollution. Water temperatures were recorded using data loggers and precipitation data obtained from a nearby rain gauge. The correlation structure of environmental parameters (temperature and rainfall), FIB concentrations, and A. pulchra microbiome diversity was evaluated using a structural equation model. Beta diversity analyses were used to investigate spatio-temporal trends of microbiome composition. Results: Acropora pulchra microbiome diversity differed between tissues and mucus, with mucus microbiome diversity being similar to the surrounding seawater. Rainfall and associated fluctuations of FIB concentrations were correlated with changes in tissue and mucus microbiomes, indicating their role as drivers of A. pulchra microbiome diversity. A. pulchra tissue microbiome composition remained relatively stable throughout dry and wet seasons; tissues were dominated by Endozoicomonadaceae, coral endosymbionts and putative indicators of coral health. In nearshore A. pulchra tissue microbiomes, Simkaniaceae, putative obligate coral endosymbionts, were more abundant than in A. pulchra colonies growing near the reef crest (farshore). A. pulchra mucus microbiomes were more diverse during the wet season than the dry season, a distinction that was also associated with drastic shifts in microbiome composition. This study highlights the seasonal dynamics of coral microbiomes and demonstrates that microbiome diversity and composition may differ between coral tissues and the surface mucus layer.

Insights on kraft lignin degradation in an anaerobic environment.

Lignin is an aromatic macromolecule and one of the main constituents of lignocellulosic materials. Kraft lignin is generated as a residual by-product of the lignocellulosic biomass industrial process, and it might be used as a feedstock to generate low molecular weight aromatic compounds. In this study, we seek to understand and explore the potential of ruminal bacteria in the degradation of kraft lignin. We established two consortia, KLY and KL, which demonstrated significant lignin-degrading capabilities. Both consortia reached maximum growth after two days, with KLY showing a higher growth and decolorization rate. Additionally, SEM analysis revealed morphological changes in the residual lignin from both consortia, indicating significant degradation. This was further supported by FTIR spectra, which showed new bands corresponding to the C-H vibrations of guaiacyl and syringyl units, suggesting structural transformations of the lignin. Taxonomic analysis showed enrichment of the microbial community with members of the Dickeya genus. Seven metabolic pathways related to lignin metabolism were predicted for the established consortia. Both consortia were capable of consuming aromatic compounds such as 4-hydroxybenzoic acid, syringaldehyde, acetovanillone, and syringic acid, highlighting their capacity to convert aromatic compounds into commercially valuable molecules presenting antifungal activity and used as food preservatives as 4-hydroxyphenylacetic, 3-phenylacetic, and phenylacetic acids. Therefore, the microbial consortia shown in the present work are models for understanding the process of lignin degradation and consumption in bacterial anaerobic communities and developing biological processes to add value to industrial processes based on lignocellulosic biomass as feedstock.