Differences In Bacterial Community Composition Research Articles

Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds

BackgroundAnimal bacterial symbionts are established early in life, either through vertical transmission and/or by horizontal transmission from both the physical and the social environment, such as direct contact with con- or heterospecifics. The social environment particularly can influence the acquisition of both mutualistic and pathogenic bacteria, with consequences for the stability of symbiotic communities. However, segregating the effects of the shared physical environment from those of the social interactions is challenging, limiting our current knowledge on the role of the social environment in structuring bacterial communities in wild animals. Here, we take advantage of the avian brood-parasite system of Eurasian magpies (Pica pica) and great spotted cuckoos (Clamator glandarius) to explore how the interspecific social environment (magpie nestlings developing with or without heterospecifics) affects bacterial communities on uropygial gland skin.ResultsWe demonstrated interspecific differences in bacterial community compositions in members of the two species when growing up in monospecific nests. However, the bacterial community of magpies in heterospecific nests was richer, more diverse, and more similar to their cuckoo nest-mates than when growing up in monospecific nests. These patterns were alike for the subset of microbes that could be considered core, but when looking at the subset of potentially pathogenic bacterial genera, cuckoo presence reduced the relative abundance of potentially pathogenic bacterial genera on magpies.ConclusionsOur findings highlight the role of social interactions in shaping the assembly of the avian skin bacterial communities during the nestling period, as exemplified in a brood parasite—host system.

Oxygen regulation of microbial communities and chemical compounds in cigar tobacco curing.

Curing is a critical process that determines the sensory quality of cigars. The impact of oxygen on cigar curing and the mechanisms by which it regulates microbial changes affecting cigar quality are not well understood. In this study, we selected handmade cigars from the same batch and conducted curing experiments in environments with varying oxygen concentrations (equivalent to 0.1%, 6-12, and 15% of atmospheric oxygen concentration). We collected samples over 60 days and analyzed the distribution of microbial communities using high-throughput sequencing. Combined with the analysis of total sugars, proteins, flavor substances, and other chemical compounds, we elucidated how different oxygen concentrations affect the cigar curing process, influence microbial community succession, and ultimately impact cigar quality. Our results revealed significant differences in bacterial community composition under different oxygen conditions. Under aerobic conditions, Cyanobacteria were the dominant bacteria, while under oxygen-limited conditions, Staphylococcus and Corynebacterium predominated. As oxygen concentration decreased, so did the richness and diversity of the bacterial community. Conversely, oxygen concentration had a lesser impact on fungi; Aspergillus was the dominant genus in all samples. We also found that Enterococcus showed a positive correlation with aspartic acid, alanine, and 4-aminobutyric acid and a negative correlation with cysteine. Cigars cured at 15% oxygen concentration for 60 days exhibited optimal quality, particularly in terms of flavor richness and sweetness. These findings suggest that oxygen concentration can alter cigar quality by regulating aerobic and anaerobic microbial community succession. The relationship between specific microbial communities and flavor compounds also provides a theoretical reference for developing artificial control technologies in the cigar curing process.

Differences in bacterial community composition between fish-stocked and fishless lakes from an arid Patagonian plateau

Differences in bacterial community composition between fish-stocked and fishless lakes from an arid Patagonian plateau

Metagenomic Investigation of the Short-Term Temporal and Spatial Dynamics of the Bacterial Microbiome and the Resistome Downstream of a Wastewater Treatment Plant in the Iskar River in Bulgaria.

Waste Water Treatment Plants (WWTP) aim to reduce contamination in effluent water; however, studies indicate antimicrobial resistance genes (ARGs) persist post-treatment, potentially leading to their spread from human populated areas into the environment. This study evaluated the impact of a large WWTP serving 125,000 people on the Iskar River in Bulgaria, by characterizing the spatial and short-term temporal dynamics in bacterial community dynamics and resistance profiles of the surface water. Pairs of samples were collected biweekly on four dates from two different locations, one about 800 m after the WWTP effluents and the other 10 km downstream. Taxonomic classification revealed the dominance of Pseudomonodota and Bacteriodota, notably the genera Flavobacterium, Aquirufa, Acidovorax, Polynucleobacter, and Limnohabitans. The taxonomic structure corresponded with both lentic and lotic freshwater habitats, with Flavobacterium exhibiting a significant decrease over the study period. Principal Coordinate Analysis revealed statistically significant differences in bacterial community composition between samples collected on different dates. Differential abundance analysis identified notable enrichment of Polynucleobacter and Limnohabitans. There were shifts within the enriched or depleted bacterial taxa between early and late sampling dates. High relative abundance of the genes erm(B), erm(F), mph(E), msr(E) (macrolides); tet(C), tet(O), tet(W), tet(Q) and tet(X) (tetracyclines); sul1 and sul2 (sulphonamides); and cfxA3, cfxA6 (beta-lactams) were detected, with trends of increased presence in the latest sampling dates and in the location closer to the WWTP. Of note, genes conferring resistance to carbapenems blaOXA-58 and blaIMP-33-like were identified. Co-occurrence analysis of ARGs and mobile genetic elements on putative plasmids showed few instances, and the estimated human health risk score (0.19) according to MetaCompare2.0 was low. In total, 29 metagenome-assembled genomes were recovered, with only a few harbouring ARGs. This study enhances our understanding of freshwater microbial community dynamics and antibiotic resistance profiles, highlighting the need for continued ARGs monitoring.

Determining the footprint of breeding in the seed microbiome of a perennial cereal

BackgroundSeed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays.ResultsIntermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds.ConclusionOverall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.

Long-term subsoiling and tillage rotation increase carbon storage in soil aggregates and the abundance of autotrophs

Autotrophic microorganisms in soil can increase soil carbon (C) sequestration by utilising chemical energy released from inorganic compounds to fix atmospheric CO2. Therefore, the effects of tillage systems on soil C stocks and autotrophic microbial community deserves in-depth study. The effects of five tillage systems, including no tillage (NoTill), subsoiling (SubS), rotary tillage (RotTill, local general tillage), no tillage-subsoiling-no tillage (NoTill-SubS), and rotary tillage-subsoiling-rotary tillage (RotTill-SubS) were investigated within a 17-year field experiment. Their effects on soil aggregates, C content and enzyme activities were studied, and the impacts on C-fixing microbial communities were analysed using the C-fixing gene cbbL. The macroaggregate portion and RubisCO and ATPase activities were the highest under SubS, causing the aggregate-associated organic C (AOC) to be 93 % higher than that under RotTill. Under RotTill-SubS, SOC, AOC and aggregate-associated microbial biomass C (AMBC) were larger than those under RotTill. RotTill-SubS reduced the microaggregate portion, increased enzyme activities and the relative abundance of C-fixing bacteria, including Sphingomonadales, Burkholderiales, and Nitrosomonadales. The macroaggregate portion under NoTill-SubS and the relative abundance of Sphingomonadales and Burkholderiales was the highest. Correspondingly, the SOC content was the largest (29 % higher than that in RotTill), and the AOC and AMBC contents were 42 % and 31 % larger, respectively, than those in RotTill. Structural equation modelling reveals that increasing tillage or lowering AOC content can directly increase differences in autotrophic bacterial communities. The reduced aggregate stability decreases C content and increases ATPase and RubisCO activities can indirectly increase differences in bacterial community composition.

Unveiling soil bacterial ecosystems in andean citrus orchards of Santander, Colombia

Citrus cultivation is vital to global agriculture, necessitating a comprehensive understanding of the soil microbiome’s diversity for sustainable practices. This study provides initial insights into the bacteriome in citrus crops in Santander, Colombia, employing a holistic approach combining culture-based techniques, sequencing methods, and bioinformatics analyses. The study explores organic and non-organic cultivation systems, revealing statistically significant differences in bacterial community composition between both practices. In general, the communities are dominated by members of the Actinobacteria and Proteobacteria, along with bacterial orders Gaiellales and Burkholderiales, all contributing to intricate ecological processes. Culture-based methods aided in the isolation of potential biotechnologically relevant strains. Among them, strain CP102 showed a pronounced carboxymethylcellulose (CMC) degradation capacity. Genetic analysis of the isolate resulted in the generation of the first closed genome of a member of the species Enterobacter soli and identified an unreported 109 kb plasmid. Further genomic examination revealed genes potentially associated with cellulose degradation in this species, which provides the isolate with biotechnological potential. This research significantly advances the global understanding of citrus-associated bacteriomes, shaping future agricultural practices and promoting the development of sustainable bioproducts.

Effect of Altitude Gradients on the Spatial Distribution Mechanism of Soil Bacteria in Temperate Deciduous Broad-Leaved Forests.

Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in forest ecosystems with strong altitude gradients in climate, vegetation, and soil properties. Based on dynamic site monitoring of the Baiyun Mountain Forest National Park (33°38'-33°42' N, 111°47'-111°51' E), this study used Illumina technology to sequence 120 soil samples at the site and explored the spatial distribution mechanisms and ecological processes of soil bacteria under different altitude gradients. Our results showed that the composition of soil bacterial communities varied significantly between different altitude gradients, affecting soil bacterial community building by influencing the balance between deterministic and stochastic processes; in addition, bacterial communities exhibited broader ecological niche widths and a greater degree of stochasticity under low-altitude conditions, implying that, at lower altitudes, community assembly is predominantly influenced by stochastic processes. Light was the dominant environmental factor that influenced variation in the entire bacterial community as well as other taxa across different altitude gradients. Moreover, changes in the altitude gradient could cause significant differences in the diversity and community composition of bacterial taxa. Our study revealed significant differences in bacterial community composition in the soil under different altitude gradients. The bacterial communities at low elevation gradients were mainly controlled by stochasticity processes, and bacterial community assembly was strongly influenced by deterministic processes at middle altitudes. Furthermore, light was an important environmental factor that affects differences. This study revealed that the change of altitude gradient had an important effect on the development of the soil bacterial community and provided a theoretical basis for the sustainable development and management of soil bacteria.

Difference in composition and functional analysis of bacterial communities between Mytilus galloprovincialis gills and surrounding water in a brackish inshore bay, analyzed by 16S rDNA multi-amplicon sequencing

BackgroundLagoons are important natural systems, with attractive favorable conditions for aquaculture production, such as shellfish cultivation. Despite their socio-economic relevance for human activity, information on the microbial diversity, community composition, and putative functions of gill-associated microbiota and seawater is still limited, particularly as regards the extent of specific taxa enrichment within the gills and the relative effects of the temporal and spatial variables. In this study, we used a 16S rDNA multi-amplicon sequencing approach using an Ion GeneStudio S5 System and a function prediction method (Functional Annotation of Prokaryotic Taxa (FAPROTAX), to inspect the springtime dynamics of microbial communities and their inferred metabolic features in an Adriatic lagoon (Po Delta, Italy).ResultsMussels and surrounding seawater were sampled in two rearing areas three times between April and June 2021. Sequencing results showed significant (p ≤ 0.05) differences in bacterial community composition and diversity between gills and seawater. Gills were dominated by the Methylobacterium-Methylorubrum and Burkholderia-Caballeronia-Paraburkholderia genera, while in seawater samples Izamaplasma, Planktomarina, and Candidatus Aquiluna were detected as being dominant. The microbiota composition did not differ significantly between the two rearing areas. The sampling time, although limited to a 3-month timeframe, instead revealed a structural variation of the bacterial profile both in gills and seawater for alpha and beta diversities respectively. The functional prediction analysis highlighted an overexpression of human gut-associated bacteria in relation to the season-related increase in seawater temperature.ConclusionsThese findings enhance our understanding of the differences between gill-associated and seawater microbiota composition and provide novel insights into the functions carried out by bacteria inhabiting these niches, as well as on the key host-symbiont relationships of bivalves in lagoon environments.

Biogeographic survey of soil bacterial communities across Antarctica

BackgroundAntarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs.ResultsSoil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs.ConclusionsOverall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities.APsmQ8MphSAgg4BzZyqdNTVideo

Microbial colonization and chemically influenced selective enrichment of bacterial pathogens on polycarbonate plastic.

Plastic pollution in aquatic environments poses significant concerns due to its potential to serve as a refuge for aquatic pathogens. However, the role of plastic surfaces and microbial biofilm interfaces in facilitating pathogen development remains poorly understood. In this study, a microcosm setup was employed to investigate the interactions between plastics and the microbial community and examine the differences in bacterial community composition and potential pathogen occurrences between the plastisphere-biofilm and surrounding seawater. Community composition analysis combined with SEM observations over time indicated that biofilm extracellular polymeric substance formation over 14 days had a link with the relative abundance and succession patterns of pathogen taxa. Colony clusters were observed on biofilms from day 7 and coincided with higher bacterial pathogen dominance. On day 14, pathogen abundance overall decreased with a potentially degrading biofilm. Pseudomonas and Pseudoalteromonas were the dominant potential pathogen groups observed in the microcosm. When further subjected to chemical treatment as an imposed environmental stress over time, biofilm-associated Psuedoalteromonas sharply increased in abundance after three days of exposure, but quickly diminished by 14days in favor of genera such as Acinetobacter, Pseudomonas, and Staphylococcus. These results suggest that environmental plastisphere-biofilms can promote the early selection, enrichment, and spread of pathogenic bacteria in the aquatic environment and could be later worsened under chemical and long-term pressure. This study provided new insights into the succession of pathogens in plastisphere biofilms, contributing to the understanding of pathogen risks involved in emerging plastisphere biofilms in light of global plastic pollution.

Filtration effect of Cordyceps chanhua mycoderm on bacteria and its transport function on nitrogen.

During the natural growth of Cordyceps chanhua, it will form a mycoderm structure specialized from hyphae. We found that the bacterial membrane of C. chanhua not only filters environmental bacteria but also absorbs and transports nitrogen elements inside and outside the body of C. chanhua. These findings are of great significance for understanding the stable mechanism of the internal microbial community maintained by C. chanhua and how C. chanhua maintains its own nutritional balance. In addition, this study also enriched our understanding of the differences in bacterial community composition and related bacterial community functions of C. chanhua at different growth stages, which is of great value for understanding the environmental adaptation mechanism, the element distribution network, and the changing process of symbiotic microbial system after Cordyceps fungi infected the host. At the same time, it can also provide a theoretical basis for some important ecological imitation cultivation technology of Cordyceps fungi.

Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis.

Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.

PSIII-14 Effect of Water Delivery System on Intestinal Microbial Populations of Nursery Pigs

Abstract A previous experiment was conducted to determine if cleanliness of a water delivery system influenced growth performance of nursery pigs. Additionally, we hypothesized that cleanliness of the water delivery system would alter populations of intestinal bacteria. Newly weaned pigs (n = 315; about 21 d of age) were used in a 42-d experiment and were assigned randomly to 1 of 2 water line treatments with 17 to 18 pens/treatment and 9 pigs/pen. Treatments consisted of water delivered to pens via a water distribution system in use for 21 years without cleaning (OLD) or water delivered to pens via a water distribution system in use for 6 weeks (NEW). Water for both distribution systems was sourced from a common well. Pigs were housed in an environmentally controlled, power-ventilated, confinement nursery barn and were allowed ad libitum access to water and common diets fed in 3 phases across OLD and NEW treatments. Twenty-eight pigs of average body weight (n = 14 pigs/treatment) were selected for collection of fecal swabs on days 0, 4, and 42 post-weaning. A pooled water sample was collected from 10 randomly selected pens/treatment and from the water supply on days 4 and 42. Swabs were also collected from the inside surface of each water line at the beginning and end of each line. To characterize the microbiome in all samples, extracted DNA was sequenced on the MiSeq platform targeting the V4 variable region of the 16S rRNA bacterial gene, and sequence data were analyzed using DADA2 and various packages within the R statistical software. Bacterial community composition of water and water line samples differed between OLD and NEW, while the sampling location of line swabs differed by location (PERMANOVA, R2 = 0.2-0.6, P < 0.05). No differences in alpha diversity were observed in pig fecal bacteria at d 0 or d 42 between OLD and NEW line. However, at d 4, pigs drinking water from the NEW line had increased fecal bacterial richness (P = 0.044) and a tendency for increased bacterial diversity (Shannon’s H, P = 0.059) compared with pigs drinking water from the OLD line. There were no differences in bacterial community composition between the OLD and NEW line throughout the trial; however, pigs drinking water from the NEW line showed more discriminating bacterial taxa compared with OLD at day 4 and 42, including greater abundances of Prevotella, Christensenellaceae R7, Rosburia and Bacteroides, among others (P < 0.05). In conclusion, drinking water from either water line did not have major effects on the gut microbiome of pigs, except for more fecal bacterial diversity in pigs drinking water from the new water line at day 4 post-weaning.

Change in Urinary Inflammatory Biomarkers and Psychological Health with Gut Microbiome Modulation after Six Months of a Lifestyle Modification Program in Children.

Background: Obesity is a metabolic disorder that negatively impacts the quality of life. Long-term methods such as exercise and low-fat diets can help regulate this health issue, but 93.3 million Americans continue to struggle. Our research investigates if lifestyle changes can affect urinary inflammation markers and psychological aspects through the modification of gut microbiome composition. Methods: Our study included 16 healthy controls with normal BMI as a comparison group and 22 overweight/obese (OW/OB) adolescents. We collected demographic, clinical, psychological, stool, and urine sample data at enrollment and six months after implementing lifestyle modifications. Bacterial genomic data and inflammatory markers in these samples were analyzed. Results: The lifestyle interventions were associated with decreased inflammation and enhanced mental health among overweight teens. We observed differences in bacterial community compositions between healthy participants and those who underwent treatment, including exercise and dietary habit adjustments, although there was no significant change in bacterial species richness. Mental health correlated with gut microbiota compositions without any demographic influences. The research also uncovered connections between inflammatory markers, psychological factors, and gut microbiota phyla through carbohydrate metabolism alterations. Conclusion: Our findings demonstrate that lifestyle modifications are associated with improved mental health and a reduction in inflammation in overweight adolescents by adjusting the gut microbiota composition.

Soil Bacterial Community Structure and Function Prediction of Millet/Peanut Intercropping Farmland in the Lower Yellow River

The objective of this study was to explore the microecological variability in farmland soil fertility in response to millet-peanut intercropping patterns by clarifying the effects of millet-peanut 4:4 intercropping on soil bacterial community structure and its diversity, as well as to provide a reference basis for promoting ecological restoration and arable land quality improvement in the lower Yellow River farmland. The Illumina MiSeq high-throughput sequencing technology and QIIME 2 platform were used to analyze the differences in bacterial community composition and their influencing factors in five soils[sole millet (SM), sole peanut (SP), intercropping millet (IM), intercropping peanut (IP), and millet-peanut intercropping (MP)] and to predict their ecological functions. The results showed that the α-diversity of intercropping soil bacterial communities differed from that of monocropping, though not significantly, whereas the β-diversity was significantly different (P<0.05). A total of 7081 ASVs were obtained from all soil samples, classified into 34 phyla, 109 orders, 256 class, 396 families, 710 genera, and 1409 species, of which 727 ASVs were shared, accounting for 24.5% to 27.8% in five soil species. The bacterial communities of millet-peanut intercropping and its monocropping soils were similar in phylum composition but varied in relative abundance. All five soils were dominated by the Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, with a relative abundance of 79.40%-81.33%. Soil organic carbon and alkaline nitrogen were the most important factors causing differences in the structures of the five soil bacterial communities at the phylum and genus levels, respectively. The PICRUSt functional prediction revealed that the relative abundance of primary functional metabolism was the largest (78.9%-79.3%), and the relative abundance of secondary functional exogenous biodegradation and metabolism fluctuated the most (CV=3.782%). In terms of the BugBase phenotype, the relative abundance of oxidative stress-tolerant bacteria increased in intercropping millet or peanut soils compared to that in the corresponding monocultures and significantly increased in intercropping millet soils compared to that in sole millet (P<0.05). Oxidative stress-tolerant, Gram-positive, and aerobic phenotypes were highly significantly positively correlated with each other (P<0.01), and all three showed highly significant negative correlations with potential pathogenicity and Gram-negative and anaerobic phenotypes (P<0.01). This showed that millet-peanut intercropping resulted in differences in soil bacterial community diversity, abundance, and metabolic functions and the possibility of reducing the occurrence of potential soil diseases. It can be used to regulate the soil microbiological environment to promote ecological restoration and sustainable development of farmland in the lower Yellow River.

Phytoplankton Producer Species and Transformation of Released Compounds over Time Define Bacterial Communities following Phytoplankton Dissolved Organic Matter Pulses.

Phytoplankton-bacterium interactions are mediated, in part, by phytoplankton-released dissolved organic matter (DOMp). Two factors that shape the bacterial community accompanying phytoplankton are (i) the phytoplankton producer species, defining the initial composition of released DOMp, and (ii) the DOMp transformation over time. We added phytoplankton DOMp from the diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 to natural bacterial communities from the eastern Mediterranean and determined the bacterial responses over a time course of 72 h in terms of cell numbers, bacterial production, alkaline phosphatase activity, and changes in active bacterial community composition based on rRNA amplicon sequencing. Both DOMp types were demonstrated to serve the bacterial community as carbon and, potentially, phosphorus sources. Bacterial communities in diatom-derived DOM treatments maintained higher Shannon diversities throughout the experiment and yielded higher bacterial production and lower alkaline phosphatase activity compared to cyanobacterium-derived DOM after 24 h of incubation (but not after 48 and 72 h), indicating greater bacterial usability of diatom-derived DOM. Bacterial communities significantly differed between DOMp types as well as between different incubation times, pointing to a certain bacterial specificity for the DOMp producer as well as a successive utilization of phytoplankton DOM by different bacterial taxa over time. The highest differences in bacterial community composition with DOMp types occurred shortly after DOMp additions, suggesting a high specificity toward highly bioavailable DOMp compounds. We conclude that phytoplankton-associated bacterial communities are strongly shaped by the phytoplankton producer as well as the transformation of its released DOMp over time. IMPORTANCE Phytoplankton-bacterium interactions influence biogeochemical cycles of global importance. Phytoplankton photosynthetically fix carbon dioxide and subsequently release the synthesized compounds as dissolved organic matter (DOMp), which becomes processed and recycled by heterotrophic bacteria. Yet the importance of phytoplankton producers in combination with the time-dependent transformation of DOMp compounds on the accompanying bacterial community has not been explored in detail. The diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 belong to globally important phytoplankton genera, and our study revealed that DOMp of both species was selectively incorporated by the bacterial community. The producer species had the highest impact shortly after DOMp appropriation, and its effect diminished over time. Our results improve the understanding of the dynamics of organic matter produced by phytoplankton in the oceans as it is utilized and modified by cooccurring bacteria.

Water temperature and organic carbon control spatio‐temporal dynamics of particle‐attached and free‐living bacterial communities in a hypereutrophic urban river network

Abstract Bacteria are an important component of the aquatic ecosystem playing a key role in the transformation and mineralisation of allochthonous organic matter, nutrients and pollutants. However, there is no clear understanding of spatio‐temporal patterns of particle‐attached versus free‐living bacterial abundances, diversities and communities, which limits our in‐depth understanding of hypereutrophic urban river ecosystems and the mechanisms regulating nutrient cycling and biogeochemical transformations. In order to investigate spatio‐temporal patterns and associated factors for aquatic particle‐attached versus free‐living bacterial communities, we conducted a 2‐year study of four contrasting habitats in a hypereutrophic urban river network of eastern China. Bacterial abundance and community structure in relation to various environmental variables were assessed by epifluorescence microscopy and high‐throughput sequencing techniques. Results revealed that particle‐attached bacterial abundance depended mainly on suspended particle concentrations, whereas free‐living bacterial abundance was correlated with nutrient availability and water temperature. Organic carbon was related to a decrease of free‐living and particle‐attached bacterial richness, and particulate matter input increased free‐living bacterial diversity. Seasonal changes of water temperature were linked to the temporal dynamics of bacterial community composition, and the differences in total organic carbon concentrations contributed to spatial differences in bacterial community composition. There were significant differences in bacterial community composition between particle‐attached and free‐living assemblages in low‐turbidity/low‐nutrient rivers found in land areas comprising mainly natural vegetation. These differences were especially prominent for the relative abundances of Cyanobacteria and Actinobacteria, which were higher in the particle‐attached and free‐living fractions, respectively. However, no significant differences were found in turbid/nutrient‐rich rivers. Total organic carbon was the most significant factor shaping the composition similarity between particle‐attached and free‐living bacterial communities. Our findings indicate that spatio‐temporal variations in water temperature, suspended particle and resource availability, especially for organic carbon, appreciably contribute to changes in the abundance, diversity and composition of aquatic particle‐attached versus free‐living bacterial communities in the hypereutrophic urban river network. Considering that biodiversity is important for supporting ecosystem functioning, this study informs spatio‐temporal patterns of particle‐attached and free‐living bacterial abundance, diversity and composition of communities, and their underlying control mechanisms, thereby providing fundamental knowledge of microbial ecological functions for remediation and sustainable management of hypereutrophic urban river ecosystems.

Dynamics of Bacterial Communities by Apple Tissue: Implications for Apple Health.

Herein, we explored the potential of the apple's core microbiota for biological control of Erwinia amylovora, which causes fire blight disease, and analyzed the structure of the apple's bacterial community across different tissues and seasons. Network analysis results showed distinct differences in bacterial community composition between the endosphere and rhizosphere of healthy apples, and eight taxa were identified as negatively correlated with E. amylovora, indicating their potential key role in a new control strategy against the pathogen. This study highlights the critical role of the apple's bacterial community in disease control and provides a new direction for future research in apple production. In addition, the findings suggest that using the composition of the apple's core taxa as a biological control strategy could be an effective alternative to traditional chemical control methods, which have been proven futile and environmentally harmful.

Characterization of bacterial communities in ticks parasitizing cattle in a touristic location in southwestern China

The purpose of this study was to investigate tick species around Mount Fanjing and analyze bacterial communities in two species – Rhipicephalus microplus and Haemaphysalis longicornis – parasitizing cattle in Tongren, Guizhou province, Southwest China, using high-throughput sequencing methods. In April 2019, ticks were collected from five sites in Jiangkou County, Yinjiang County, and Songtao County. In total, 296 ticks were collected, comprising two genera and three species: H. longicornis, Haemaphysalis flava, and R. microplus. Rhipicephalus microplus was the most representative species (57.4%) within the collected group, being the dominant species in Tongren City, followed by H. longicornis (39.5%) and H. flava (3.0%). Beta-diversity analysis revealed differences in bacterial community composition among the tick species. The bacterial community structure of R. microplus collected in the three counties was highly similar. Chlorella and Bacillus were highly abundant in H. longicornis. Rickettsia was detected at high relative abundance in R. microplus but in low relative abundance in H. longicornis, suggesting that Rickettsia is more associated with R. microplus than with H. longicornis. More in-depth investigations are needed to determine the pathogenic risk of Rickettsia and its relationship with the host. This is the first survey on tick-borne bacterial communities in this area, which is of great significance for the prevention and control of tick-borne diseases locally.