Changes In Bacterial Communities Research Articles

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars.

Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.

Inoculation with Roseovarius increases thermal tolerance of the coral photosymbiont, Breviolum minutum

Coral reefs are diverse marine ecosystems that have tremendous ecological and cultural value and support more than 25% of eukaryote marine biodiversity. Increased ocean temperatures and light intensity trigger coral bleaching, the breakdown of the relationship between corals and their photosymbionts, dinoflagellates of the family Symbiodiniaceae. This leaves corals without their primary energy source, thereby leading to starvation and, often, death. Coral bleaching is hypothesized to occur due to an overproduction of reactive oxygen species (ROS) by Symbiodiniaceae, which subsequently accumulate in coral tissues. Bacterial probiotics have been proposed as an approach to mitigate coral bleaching, by reducing ROS levels in the coral holobiont through bacterial antioxidant production. Both corals and Symbiodiniaceae are known to associate with bacteria. However, the Symbiodiniaceae-bacteria relationship, and its impact on Symbiodiniaceae thermal tolerance, remains a poorly studied area. In this study, cultured Symbiodiniaceae of the species Breviolum minutum were treated with antibiotics to reduce their bacterial load. The cultures were subsequently inoculated with bacterial isolates from the genus Roseovarius that were isolated from the same B. minutum culture and showed either high or low ROS-scavenging abilities. The B. minutum cultures were then exposed to experimental heat stress for 16 days, and their health was monitored through measurements of cell density and photochemical efficiency of photosystem II. It was found that B. minutum inoculated with Roseovarius with higher ROS-scavenging abilities showed greater cell growth at elevated temperatures, compared to cultures inoculated with a Roseovarius strain with lower ROS-scavenging abilities. This suggests that Roseovarius may play a role in Symbiodiniaceae fitness at elevated temperatures. Analysis of Symbiodiniaceae-associated bacterial communities through 16S rRNA gene metabarcoding revealed that Roseovarius relative abundance increased in B. minutum cultures following inoculation and with elevated temperature exposure, highlighting the contribution they may have in shielding B. minutum from thermal stress, although other bacterial community changes may have also contributed to these observations. This study begins to unpick the relationship between Symbiodiniaceae and their bacteria and opens the door for the use of Symbiodiniaceae-associated bacteria in coral reef conservation approaches.

Soil Microbial Community, Soil Quality, and Productivity along a Chronosequence of Larix principis-rupprechtii Forests.

Elucidating the correlation between soil microbial communities and forest productivity is the focus of research in the field of forest ecology. Nonetheless, the relationship between stand age, soil quality, soil microorganisms, and their combined influence on productivity is still unclear. In this study, five development stages (14, 25, 31, 39, and >80 years) of larch (Larix principis-rupprechtii) forests were investigated in Inner Mongolia and Shanxi provinces of China. We evaluated soil quality using the Integrated Soil Quality Index (SQI) and analyzed changes in bacterial and fungal communities using high-throughput sequencing. Regression models were also established to examine the impacts of stand age, microbial diversity, and SQI on productivity. The findings revealed an ascending trend in soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and SQI in 14, 25, 31, and 39-year-old stands. The abundance of oligotrophic bacteria Acidobacteria exhibited a gradual decline with increasing forest age, whereas copiotroph bacteria Proteobacteria displayed a progressive increase. Stands older than 80 years exhibited a higher abundance of both the saprophytic fungus Ascomycota and mycorrhizal fungus Basidiomycota. Forest age had a significant impact on microbial diversity, particularly in terms of bacterial diversity, impacting both α and β diversity. The soil bacterial community structure was influenced by AK, SOM, TN, TP, and pH. Conversely, the fungal community structure was regulated by crucial factors including SOM, TN, TP, TK, AK, and pH. Fungal diversity demonstrated a significant and positive correlation with the basal area increment (BAI) of larch. Furthermore, microbial diversity accounted for 23.6% of the variation in BAI. In summary, the findings implied a robust association between microbial composition, diversity, and soil chemical properties throughout the chronosequence of larch forests. These factors collectively played a crucial role in influencing the productivity of larch forest.

Effects of Biochar Application on Physicochemical Properties and Bacterial Communities of Microplastic-contaminated Calcareous Soil

Microplastics are widely distributed in the soil environment, threatening the soil ecological environment system and changing soil physicochemical properties and microbial characteristics. Biochar is often used as a soil amendment to improve soil quality due to its special pore structure and good soil nutrient retention ability. However, the understanding of the effects and mechanisms of biochar application on the physicochemical properties and bacterial communities of microplastic-contaminated soils is still very limited. Therefore, a 21-day micro-soil culture experiment was conducted to analyze the effects of biochar application on physicochemical properties and bacterial community changes in soil contaminated with different concentrations of microplastics using 16S rRNA high-throughput sequencing technology. The results revealed that the application of biochar slowed down the decrease in nitrate nitrogen and Olsen-P contents in microplastic-contaminated soil and increased the total phosphorus content. Biochar addition increased the relative abundance of tolerant phylum such as Acidobacteriota, Actinobacteriota, and Bacteroidota in microplastic-contaminated calcareous soil. Proteobacteria, Acidobacteriota, and Actinobacteriota were the dominant bacteria of the soil bacterial community in each treatment on day 7 and day 21. Compared with that on day 7, the relative abundance of Proteobacteria and Firmicutes significantly decreased, and the relative abundance of Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Myxococcota increased on day 21. Biochar application also increased the relative abundance of Lysobacter in microplastic-contaminated soils. This study demonstrated that the application of biochar increased microplastic-resistant bacteria, enhanced the stability of microplastic-contaminated soil, and slowed down the pollution of microplastics to the soil. Moreover, biochar had great potential to improve the quality of microplastic-contaminated calcareous soil.

The microbial mechanisms by which long-term heavy metal contamination affects soil organic carbon levels

Globally, reducing carbon emissions and mitigating soil heavy metal pollution pose pressing challenges. We evaluated the effects of lead (Pb) and cadmium (Cd) contamination in the field over 20 years. The five treatment groups featured Pb concentrations of 40 and 250 mg/kg, Cd concentrations of 10 and 60 mg/kg, and a combination of Pb and Cd (60 and 20 mg/kg, respectively); we also included a pollution-free control group. After 20 years, soil pH decreased notably in all treatments, particularly by 1.02 in Cd10-treated soil. In addition to the increase of SOC in Cd10 and unchanged in Pb40 treatment, the SOC was reduced by 9.62%–12.98% under the other treatments. The α diversities of bacteria and fungi were significantly changed by Cd10 pollution (both p < 0.05) and the microbial community structure changed significantly. However, there were no significant changes in bacterial and fungal communities under other treatments. Cd10 pollution reduced the numbers of Ascomycota and Basidiomycota fungi, and enhanced SOC accumulation. Compared to the control, long-term heavy Cd, Pb, and Pb–Cd composite pollution caused SOC loss by increasing Basidiomycota which promoting carbon degradation, and decreasing Proteobacteria which promoting carbon fixation via the Krebs cycle. Our findings demonstrate that heavy metal pollution mediates Carbon-cycling microorganisms and genes, impacting SOC storage.

Enhance of tomato production and induction of changes on the organic profile mediated by Rhizobium biofortification.

The extensive use of chemical fertilizers has served as a response to the increasing need for crop production in recent decades. While it addresses the demand for food, it has resulted in a decline in crop productivity and a heightened negative environmental impact. In contrast, plant probiotic bacteria (PPB) offer a promising alternative to mitigate the negative consequences of chemical fertilizers. PPB can enhance nutrient availability, promote plant growth, and improve nutrient uptake efficiency, thereby reducing the reliance on chemical fertilizers. This study aimed to evaluate the impact of native Rhizobium strains, specifically Rhizobium calliandrae LBP2-1, Rhizobium mayense NSJP1-1, and Rhizobium jaguaris SJP1- 2, on the growth, quality, and rhizobacterial community of tomato crops. Various mechanisms promoting plant growth were investigated, including phosphate solubilization, siderophore production, indole acetic acid synthesis, and cellulose and cellulase production. Additionally, the study involved the assessment of biofilm formation and root colonization by GFP-tagged strains, conducted a microcosm experiment, and analyzed the microbial community using metagenomics of rhizospheric soil. The results showed that the rhizobial strains LBP2-1, NSJP1-1 and SJP1-2 had the ability to solubilize dicalcium phosphate, produce siderophores, synthesize indole acetic acid, cellulose production, biofilm production, and root colonization. Inoculation of tomato plants with native Rhizobium strains influenced growth, fruit quality, and plant microbiome composition. Metagenomic analysis showed increased Proteobacteria abundance and altered alpha diversity indices, indicating changes in rhizospheric bacterial community. Our findings demonstrate the potential that native Rhizobium strains have to be used as a plant probiotic in agricultural crops for the generation of safe food and high nutritional value.

Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting.

Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.

Changes in bacterial communities in chilled American lobster (Homarus americanus) tissues following mortality

Studies evaluating bacteria growing on dead American lobster (Homarus americanus) are typically based on a single observation of the post-mortem period. In this study, seventy-five lobsters were euthanized to evaluate changes in microbiological composition between sexes, and in gut, tail, and claw tissues over a 4-day period under chilled (4 °C) storage. The hygienic quality of meat decreased over the storage period but remained acceptable (<6 log CFU/g). Metagenomic analysis showed alpha and beta diversity differed by tissue type throughout storage time. Photobacterium spp. Were the primary spoilage bacteria identified in gut (49%) and tail (89%) but were less abundant in the claw (11%). Photobacterium spp. Abundance were unchanged in the gut over the sampling period, whereas their proportion increased in the tail (62%) and claw (32%) over the sampling period. Unlike other studies, Photobacterium phosphoreum was the predominant species detected. The detection of bacteria not previously reported in American lobster suggest there could be an association between the microbiota in lobster tissues with their diet and/or habitat, and these factors could influence the spoilage bacteria inhabiting these tissues. Findings identify an opportunity to recover tail and claw meat from dead lobsters with a quality acceptable for human consumption.

Experimentally determined traits shape bacterial community composition one and five years following wildfire.

Wildfires represent major ecological disturbances, burning 2-3% of Earth's terrestrial area each year with sometimes drastic effects above- and belowground. Soil bacteria offer an ideal, yet understudied system within which to explore fundamental principles of fire ecology. To understand how wildfires restructure soil bacterial communities and alter their functioning, we sought to translate aboveground fire ecology to belowground systems by determining which microbial traits are important post-fire and whether changes in bacterial communities affect carbon cycling. We employed an uncommon approach to assigning bacterial traits, by first running three laboratory experiments to directly determine which microbes survive fires, grow quickly post-fire and/or thrive in the post-fire environment, while tracking CO2 emissions. We then quantified the abundance of taxa assigned to each trait in a large field dataset of soils one and five years after wildfires in the boreal forest of northern Canada. We found that fast-growing bacteria rapidly dominate post-fire soils but return to pre-burn relative abundances by five years post-fire. Although both fire survival and affinity for the post-fire environment were statistically significant predictors of post-fire community composition, neither are particularly influential. Our results from the incubation trials indicate that soil carbon fluxes post-wildfire are not likely limited by microbial communities, suggesting strong functional resilience. From these findings, we offer a traits-based framework of bacterial responses to wildfire.

Regulation of soil enzyme activity and bacterial communities by food waste compost application during field tobacco cultivation cycle

Food waste (FW) composting is an effective waste resource utilization method; however, only limited approaches of FW compost application in agriculture have been investigated. This study reports changes in soil chemical properties, enzyme activities, and bacterial communities at different tillage stages and its effects on tobacco biomass after FW compost application in tobacco cultivation field experiments. The results showed that FW compost increased tobacco biomass. Also, FW compost functioned as a fertilizer that acted mainly during the maturity (September) and fallow (December) periods of tobacco, and its effect was enhanced with increasing application rates. FW compost significantly increased soil pH, organic carbon, total nitrogen, total phosphorus, alkaliolytic nitrogen, and available phosphorus content. It enhanced soil urease, acid phosphatase, fluorescein diacetate hydrolase, and polyphenol oxidase activities. FW compost application increased soil bacterial diversity, increasing the relative abundance of dominant bacteria such as Proteobacteria and Bacteroidetes while decreasing the relative abundance of Acidobacteria and Chloroflexi. Bacterial chemoheterotrophy, aerobic_chemoheterotrophy, ureolysis, chloroplasts, nitrogen_fixation, and fermentation functions were enhanced, and the complexity of ecological networks among bacterial species increased. A combined ranking analysis showed that the soil's available phosphorus, pH, alkaline nitrogen, and total phosphorus content were the main factors influencing bacterial population dynamics. In conclusion, FW composts can be used as an alternative to fertilizers. They exerts their beneficial properties by regulating bacterial communities mainly through soil chemistry, indirectly enhancing soil enzyme activity, and increasing tobacco yield.

Grazing practices affect phyllosphere and rhizosphere bacterial communities of Kobresia humilis by altering their network stability

The primary utilization strategy for meadow grasslands on the Qinghai-Tibet Plateau (QTP) is livestock grazing. This practice is considered as one of the major drivers of plant-associated bacterial community construction and changes in soil properties. The species of Kobresia humilis is considered as the most dominant one in grasslands. However, how different grazing practices affect the phyllosphere and rhizosphere bacterial communities of K. humilis is unknown. To address this issue, the effects of the grazing enclosure (GE), single-species grazing (YG and SG, representing yak only and sheep only, respectively), and different ratios of grazing (ratio of yak to sheep is 1:2, 1:4, and 1:6, represented by MG1:2, MG1:4, and MG1:6, respectively) on the dominant plant of K. humilis, it's phyllosphere and rhizosphere bacteria, and soil properties were investigated using artificially controlled grazing and grazing enclosure. Our data showed that grazing enclosure enhanced vegetation coverage, and rhizosphere bacterial richness and diversity, while reduced plant number and bacterial network stability of K. humilis. The NO3−-N, K+, and Cl− concentrations were lower under grazing compared to GE. SG reduced the concentration of NH4+-N, TN, K+, and Na+ compared to YG. Moderate grazing intensity had a lower relative abundance of the r-strategists (Bacteroidota and Gammaproteobacteria) with higher bacterial network stability. Yak and sheep grazing showed reversed impacts on the bacterial network stability between the phyllosphere and rhizosphere of K. humilis. Proteobacteria and Actinobacteriota were identified in the molecular ecological network analysis as keystone taxa in the phyllosphere and rhizosphere networks, respectively, under all treatments. This study explained why sheep grazing has more adverse effects on grazing-tolerant grass species, K. humilis, than yak grazing, and will contribute to a better understanding of the impacts of different grazing practices and grazing enclosure on alpine grassland ecosystems on the QTP.

Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation.

Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.

Succession of bacterial community structure in response to a one-time application of biochar in barley rhizosphere and bulk soils

Biochar is often used as an amendment to enhance soil fertility by directly increasing soil pH and nutrient availability. However, biochar may also improve soil fertility indirectly by altering the succession of bacterial communities that, in turn, may alter nutrient supply and availability. To determine how biochar affects soil bacterial richness and diversity, as well as how bacterial communities respond to biochar across space and time, we studied the rhizosphere and bulk soils of potted barley plants for 2 years. Adding biochar significantly increased bacterial community richness (Chao 1 richness index) by the end of the second year in the rhizosphere (P = 0.037), but in bulk soils, we observed an increase in richness in Year 1 that dissipated by Year 2. In contrast to richness, adding biochar only had a significant effect on bacterial community diversity (Shannon diversity index) in Year 1 seedling stage (P &amp;lt; 0.001), but the effect dissipated thereafter. We also found that adding biochar increased the relative abundances of Actinobacteria and Proteobacteria but decreased the relative abundances of Acidobacteria and Chloroflexi, suggesting these communities were sensitive to biochar inputs. The biochar-sensitive genera belonging to Actinobacteria and Proteobacteria made up 45%–58% of sensitive taxa in both rhizosphere and bulk soils. Of the Proteobacteria sensitive to adding biochar, Nitrosospira and Sphingomonas were most abundant in the rhizosphere relative to bulk soils. However, despite the initial increase of biochar sensitive responders in the rhizosphere, their numbers decreased after 2 years and had 179 fewer genera than bulk soils. Our findings suggest the effect of adding biochar was relatively short-lived and that the influence of the plant phenology was a stronger driver of bacterial community change than biochar inputs 2 years after its application. Altogether, the succession of soil bacterial community structure reflected changes in the soil environment induced by the combined effect of biochar, rhizospheric inputs, and plant phenology, suggesting that changes in microbial community composition observed after amending soils with biochar, may also contribute to changes in soil fertility.

Variations in diversity, composition, and species interactions of soil microbial community in response to increased N deposition and precipitation intensity in a temperate grassland

BackgroundGlobal climate change has resulted in precipitation regimes exhibiting an increasing trend in rainfall intensity but a reduction in frequency. In addition, nitrogen (N) deposition occurs simultaneously in arid and semi-arid regions. Microbial biomass, diversity, composition, and species interactions are key determinants of ecological functions. We examined the effects of changes in precipitation intensity and N addition on the soil bacterial and fungal communities in a semi-arid grassland in Inner Mongolia, China.MethodsThe microbial biomass (bacterial PLFAs and fungal PLFAs) was determined through phospholipid fatty acid (PLFA) analysis, and microbial diversity (Shannon index and evenness index) was determined with high-throughput sequencing (16S and ITS). Species interactions were determined using a molecular ecological network analysis. The relationships between microbial community (bacterial community and fungal community) and environmental variables were examined by Mantel tests.ResultsWe found that N addition decreased fungal PLFA under moderate, high, and extreme precipitation intensity treatments and increased fungal community complexity under the high precipitation intensity treatment. Furthermore, N addition increased bacterial diversity under moderate and high precipitation intensity treatments. N addition caused greater environmental stress to the fungal community, which was dominated by deterministic processes.ConclusionsThe effects of N deposition on soil bacterial and fungal communities were altered by precipitation intensity. The changes in soil bacterial and fungal communities were different, implying that composition and functional traits adapt differently to projected global changes at a regional scale.

Persistence of human- and cattle-associated Bacteroidales and mitochondrial DNA markers in freshwater mesocosms

Accurate identification of the origins of non-point source pollution is essential for the effective control of fecal pollution. Host-associated Bacteroidales and mitochondrial DNA (mtDNA) markers have been developed to identify the sources of human and cattle fecal pollution. However, the differences in persistence between these two types of markers under different environmental conditions are still poorly understood. Here, we conducted mesocosm experiments to investigate the influence of indigenous microbiota and nutrients on the decay of Bacteroidales and mtDNA markers associated with humans and cattle. Raw sewage or cattle feces were inoculated into mesocosms containing natural eutrophic water, sterile eutrophic water or artificial freshwater. The Bacteroidales markers HF183 (human) and CowM3 (cattle) and mtDNA markers HcytB (human) and QMIBo (cattle) were quantified using the quantitative polymerase chain reaction (qPCR) assays. All markers but HF183 decreased the fastest in the presence of indigenous microbiota. Nutrients caused a decrease in the persistence of HF183; however, no significant nutrient effects were observed for HcytB, CowM3, and QMIBo. The time to reach one log reduction (T90) for HF183 and HcytB was similar; CowM3 reached T90 earlier than QMIBo in all the treatments but eutrophic water. E. coli persisted longer than both Bacteroidales and mtDNA markers in the mesocosms regardless of inoculum type. Additionally, 16S rRNA gene amplicon sequencing was used to determine the changes in bacterial communities accompanying the marker decay. Analysis using the SourceTracker software showed that bacterial communities in the mesocosms became more dissimilar to those in the corresponding inoculants over time. Our results indicate that environmental factors are important determinants of genetic markers' persistence, but their impact can vary depending on the genetic markers. The cattle Bacteroidales markers may be more suitable for determining recent fecal contamination than cattle mtDNA.

Changes in Physicochemical Properties and Bacterial Communities of Tropical Soil in China under Different Soil Utilization Types

The primary purpose of our study is to clarify the differences in physicochemical properties and microbial community composition with the continuous evolution of soil utilization types. Here, we used natural forest soil (NS), healthy banana garden soil (HS), diseased banana garden soil (DS), and paddy soil (PS) in tropical areas of Hainan Province to conduct this study. According to our research, the abundance and diversity of soil bacteria (HS/DS and PS) decrease significantly as soil utilization types evolve. In healthy banana soil, the amount of Actinobacteria and Firmicutes at the bacterial phylum level is more significant than in other soil utilization types. It was observed that the bacterial community structure in NS was notably distinct from that in HS and PS. Apart from paddy soil, the bacterial makeup of the other two soil utilization types mainly remained consistent. Pathogenic soil (DS) undergoes significant changes in its chemical properties. These changes are primarily seen as decreased pH and organic carbon content and increased C/N and inorganic nitrogen content (NH4+, NO3−). This suggests that a specific type of microorganism (Fusarium oxysporum f. sp. cubense) can cause a significant shift in the soil environment, leading to an unexpected change in soil type. Therefore, to ensure that the soil is healthy, we must balance the soil microbial community composition, promote the increase of the beneficial microbial species and quantity, and create an environment suitable for microbial growth.

Rhizosphere bacterial community composition was significantly affected by continuous cropping but not by sesame genotype

Imbalanced soil bacterial community is thought to be a crucial factor for continuous cropping obstacle. Through analyzing bacterial community by Illumina MiSeq technology, this study bacterial community diversity and richness, like Sobs, Ace and PD decreased with duration of continuous cropping (CC). Alpha diversity and principal coordinate analysis (PCoA) revealed that soil bacterial diversity and community structure were significantly affected by CC but not by genotype. With increasing years of CC, rhizosphere bacterial community changed gradually, rather than skipping or irregular change. Almost all significantly changed genera under CC belong to Chloroflexi, Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes, which indicated the vital roles of these five phyla in CC. With extension of CC, the abundance of Variibacter, Candidatus_Solibacter decreased, while Sinomonas and Burkholderia-Paraburkholderia increased in the genus level. Additionally, the transport and metabolism of amino acid and carbohydrate were increased or maintained under CC, but vesicular transport and cell motility reduced. These data provided novel insights into the changes of bacterial community under short duration of CC, and will contribute to understanding of continuous cropping.

Changes of soil bacterial community, network structure, and carbon, nitrogen and sulfur functional genes under different land use types

Soil microorganisms participate in almost all soil ecological processes and are essential in maintaining ecosystem functions and terrestrial carbon, nitrogen, and sulfur cycles. Soil bacterial communities, networks, biogeochemical cycles, and land use types influence it. However, there are few studies on the changes in these indicators and their influencing factors under different land use types. Taking Dongting Lake watershed as an example, high-throughput sequencing technology combined with FAPROTAX were used to analyze the characteristics and influencing factors of soil bacterial community, network structure, and C, N, and S cycle function genes under different land use conditions. Land use types include paddy fields (PF), garden plots (GP), woodland (WL), and sloped arable land (SAL). PLS-PM model and redundancy analysis method were used to study the mechanism of soil bacterial community, network structure, functional genes, and environmental variables. The results showed that the relative abundance of dominant phylum and dominant fungi changed significantly in different land use types. The first three dominant gates in WL had the most considerable abundance and the most extensive diversity index of PF. The symbiotic network of PF has the most effective connectivity and average degree, the minor network diameter, the most complex network structure, and fierce competition among species within the same ecological niche. The results of functional genes showed that different land use types significantly changed the abundance of soil C, N, and S cycle functional genes, and soil bacteria predicted the highest abundance of functional genes in GP. C, N, and S circulating function genes were significantly correlated with pH, soil nutrients, and soil texture (P < 0.05). PLS-PM model and redundancy analysis showed that soil pH was the main factor affecting the bacterial community, network structure, and functional genes, followed by soil nutrients.

Changes of bacterial communities of rainbow trout (Oncorhynchus mykiss) at different processing steps in the production of burgers and their storage life enhancement by an acetate-based preservative

Fresh trout (Oncorhynchus mykiss) is a healthy and nutritious food which can be used for formulating ready-to-cook fish preparations, such as trout burgers. To investigate the impact of processing and the use of an acetate-based preservative on the spoilage microbiota and storage life of burgers, the dynamics of microbial communities were examined by using a combination of culture-dependent/independent techniques, Monte Carlo simulation, and PICRUSt2 analysis. Results of the microbial community analyses showed that most of the taxa of trout were lost during processing into burgers. Along the processing steps, an increase of contamination, with Flavobacterium and Pseudomonas becoming the most relative abundant genera in pulp and burgers, respectively, was observed. The Pseudomonas dynamic pattern was supported by the Monte Carlo simulation, which gave a picture of the bacterial transfer. Verdad® N6, which is a commercially available acetate-rich fermentate, was evaluated as preservative treatment for burgers during their storage life. Pseudomonas dominated the microbial community of stored burgers, irrespective of the treatment. However, their levels were lower in the fermentate-treated samples, which presented Lactobacillus as the second most relative abundant genus. PICRUSt2 analysis showed that Pseudomonas-correlated metabolic pathways of hexitol fermentation were significantly lower at the end of the storage period in burgers supplemented with the fermentate, corroborating Pseudomonas minor contribution to the metabolic activity. In summary, Verdad® N6, through its inhibiting effects on spoilage bacteria is an option for producing burgers with increased storage life.

Phenylalanine-mediated changes in the soil bacterial community promote nitrogen cycling and plant growth

Soil amino acids (AAs) are the most active components of soil N, which can be mineralized or absorbed by bacteria as N and C sources. We hypothesized that exogenous AAs could regulate the bacterial community and affect soil N cycling, and the effect sizes could vary depending on individual AAs. Here, we applied feather (keratin)-based compost rich in AAs to Poncirus trifoliata (L.) to evaluate the regulation of bacterial community by AAs; furthermore, we applied six individual AAs to test their effects. The compost significantly increased soil hydrolysable AA content, ammonia monooxygenase gene abundance, and plant growth and changed bacterial community structure. Redundancy analysis revealed that the effects of AAs on the bacterial community composition were greater than those of soil chemical properties, and phenylalanine (Phe) was the most effective among thirteen individual AAs. When applied individually, Phe caused the greatest increase in N cycling-related enzyme activity and plant growth and most significantly altered the bacterial community structure among the six exogenous AAs. Notably, Phe significantly increased the relative abundances of Burkholderia-Caballeronia-Paraburkholderia, Azospirillum, Cupriavidus, and Achromobacter, whose abundances were significantly positively correlated with plant biomass, and significantly reduced the relative abundances of Arachidicoccus, Pseudopedobacter, Sphingobacterium, and Paenibacillus, whose abundances were significantly negatively correlated with plant biomass. We demonstrate that soil AAs strongly shape the bacterial community. Particularly, Phe enhances N cycling and plant growth by increasing the potentially beneficial bacterial taxa and inhibiting the potentially harmful bacterial taxa, which needs further validation.