Bacterial Traits Research Articles

Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis.

Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.

Virulence, phenotype and genotype characteristics of invasive group B Streptococcus isolates obtained from Swedish pregnant women and neonates

Group B streptococci (GBS) are bacteria that can cause preterm birth and invasive neonatal disease. Heterogeneous expression of virulence factors enables GBS to exist as both commensal bacteria and to become highly invasive. A molecular epidemiological study comparing GBS bacterial traits, genotype and host characteristics may indicate whether it is possible to predict the risk of perinatal invasive GBS disease and more accurately target intrapartum antibiotic prophylaxis. A total of 229 invasive GBS isolates from Swedish pregnant women or neonates were assessed for virulence and phenotypic traits: hemolysis zone, hemolytic pigment (Granada agar), Streptococcus B Carrot Broth (SBCB) assay, CAMP factor, and hyaluronidase activity. Genes regulating hemolytic pigment synthesis (covR/covS, abx1, stk1, stp1) were sequenced. Of the virulence factors and phenotypes assessed, a Granada pigment or SBCB score ≥ 2 captured more than 90% of EOD isolates with excellent inter-rater reliability. High enzyme activity of hyaluronidase was observed in 16% (36/229) of the invasive GBS isolates and notably, in one case of stillbirth. Hyaluronidase activity was also significantly higher in GBS isolates obtained from pregnant/postpartum individuals versus the stillbirth or neonatal invasive isolates (p < 0.001). Sequencing analysis found that abx1 (g.T106I), stk1 (g.T211N), stp1 (g.K469R) and covS (g.V343M) variants were present significantly more often in the higher (Granada pigment score ≥ 2) versus lower pigmented isolates (p < 0.001, each variant). Among the 203 higher Granada pigment scoring isolates, 22 (10.8%) isolates had 3 of the four sequence variants and 10 (4.9%) had 2 of the four sequence variants. Although heterogeneity in GBS virulence factor expression was observed, the vast majority were more highly pigmented and contained several common sequence variants in genes regulating pigment synthesis. High activity of hyaluronidase may increase risk for stillbirth and invasive disease in pregnant or postpartum individuals. Our findings suggest that testing for GBS pigmentation and hyaluronidase may, albeit imperfectly, identify pregnant people at risk for invasive disease and represent a step towards a personalized medical approach for the administration of intrapartum antibiotic prophylaxis.

Antibiotic susceptibility and biofilm formation of Pseudomonas aeruginosa isolated from clinical and environmental hospital samples

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen and a model bacterium for studying virulence and bacterial social traits. While, it can be isolated in low numbers from a wide variety of environments including soil and water, it can readily be found in almost any human/animal-impacted environment. It is a major cause of illness and death in humans with immunosuppressive and chronic conditions and infections in these patients are difficult to treat due to a number of antibiotic resistance mechanisms and the organism’s propensity to form multicellular biofilms. One hundred twenty clinical samples and forty hospital environmental samples (various sources) were collected from hospitals in Baghdad city during the period from October 2020 to January 2021, Cetrimide agar, the differential medium was used to isolation and diagnosis of Pseudomonas aeruginosa and 76 (63.33%) clinical isolates and 8 (20%) environmental samples were able to grow, and diagnosedas P. aeruginosa using the conventional biochemical tests, the Api 20 system and 16S rRNAgene. The antibiotic susceptibility test for fourteen antibiotics was performed by the standard disk diffusion method; the results showed that the bacteria were resistant to the most of the antibiotics used in this study and have the ability to form the biofilm.

Enhanced removal of sulfur-containing organic pollutants from actual wastewater by biofilm reactor: Insights of sulfur transformation and bacterial metabolic traits

Sulfur-containing organic pollutants in wastewater could threaten human health due to their high malodor and toxicity, and their conversion processes are more complex than inorganic sulfur compounds. Membrane aerated biofilm reactor (MABR), as a novel and environmentally-friendly biofilm-based technology, is able to remove inorganic sulfur in synthetic wastewater. However, it is unknown how sulfur-containing organic pollutants in actual wastewater are transformed in MABR system. This work demonstrated the feasibility of MABR to eliminate sulfur-containing organic pollutants in actual wastewater, and the removal efficiency could be reached at approximately 100%. Meanwhile, over 70% of sulfur-containing organic contaminants were transformed to SO42− during the long-term operation. Further analysis indicated that the functional bacteria that participated in sulfur transformation and carbohydrates degradation (e.g., Chujaibacter, Microscillaceaesp., and Thiobacillus) were evidently enriched when treating actual wastewater. Moreover, the critical metabolic pathways (e.g., sulfur metabolism, glycolysis metabolism, and pyruvate metabolism), and the corresponding genetic expressions (e.g., nrrA, tauA, tauC, sorA, and SUOX) were evidently up-regulated during long-term operation, which was beneficial for the transformation of sulfur-containing organic pollutants in actual wastewater by MABR. This work would expand the application of MABR for treating the actual sulfur-containing organic wastewater and provide an in-depth understanding of the organic sulfur transformation in MABR.

Characterizing rhizosphere microbial communities associated with tolerance to aboveground herbivory in wild and domesticated tomatoes.

Root-associated microbial communities are well known for their ability to prime and augment plant defenses that reduce herbivore survival or alter behavior (i.e., resistance). In contrast, the role root microbes play in plant tolerance to herbivory, an evolutionarily sustainable alternative to resistance, is overlooked. In this study, we aimed to expand our limited understanding of what role rhizosphere microbial communities play in supporting tolerance to insect damage. Using domesticated tomatoes and their wild ancestors (Solanum spp.), we first documented how tobacco hornworm (Manduca sexta) herbivory impacted tomato fruit production in order to quantify plant tolerance. We then characterized the bacterial and fungal rhizosphere communities harbored by high and low tolerance plants. Wild tomatoes excelled at tolerating hornworm herbivory, experiencing no significant yield loss despite 50% leaf area removal. Their domesticated counterparts, on the other hand, suffered 26% yield losses under hornworm herbivory, indicating low tolerance. Ontogeny (i.e., mid- vs. late-season sampling) explained the most variation in rhizosphere community structure, with tomato line, tolerance, and domestication status also shaping rhizosphere communities. Fungal and bacterial community traits that associated with the high tolerance line include (1) high species richness, (2) relatively stable community composition under herbivory, and (3) the relative abundance of taxa belonging to Stenotrophomonas, Sphingobacterium, and Sphingomonas. Characterizing tolerance-associating microbiomes may open new avenues through which plant defenses are amended in pest management, such as plant breeding efforts that enhance crop recruitment of beneficial microbiomes.

Manure application effects on subsoils: Abundant taxa initiate the diversity reduction of rare bacteria and community functional alterations

Manure application is a significant agriculture practice that can affect the microbial community structure in both topsoil and subsoil. However, how the abundant and rare taxa in the soil profile respond to surface manure application and their ecological roles at different soil depths remain unknown. Based on a soil mesocosm experiment, we used amplicon sequencing and high-throughput quantitative-PCR array to characterize the bacterial community composition and functional traits across soil profiles. Results showed that the relative abundance and diversity of rare taxa increased in the topsoil but decreased in the 40–60 cm soil, where the relative abundance of abundant taxa increased after manure application. Evidence from network analysis, niche width and 16S rRNA operon (rrn) copy number suggest that abundant taxa in subsoils had a greater competitivity for resource mining than rare taxa. Regarding resource utilization strategies, microbial communities under manure treatment preferred to utilize recalcitrant carbon (C) and inorganic phosphorus (P) in the topsoil and labile carbon and organic phosphorus in the subsoil compared with non-manure application. Random Forest regression analysis indicated the relatively greater contribution of abundant taxa to C degradation and fixation in subsoils. These results imply that the manure application effect on microbial resource mining in subsoils is mainly driven by abundant bacteria due to the lower competitiveness of rare taxa for the C sources leached above. Overall, This study linked community functions with the ecological role of abundant and rare taxa in the context of environmental disturbances at different soil depths and shed light on the potential ecological risks of diversity reduction of subsoil rare bacteria.

Probiotic potentials of the silkworm gut symbiont Enterococcus casseliflavusECB140, a promising L-tryptophan producer living inside the host.

L-tryptophan is an essential aromatic amino acid for the growth and development of animals. Studies about enteric L-tryptophan-producing bacteria are scarce. In this report, we characterized the probiotic potential of Enterococcus casseliflavus ECB140, focusing on its L-tryptophan production abilities. ECB140 strain was isolated from the silkworm gut and can survive under strong alkaline environmental conditions. Bacterial colonization traits (motility and biofilm) were examined and showed that only ECB140 produced flagellum and strong biofilms compared with other Enterococcus strains. Comparative genome sequence analyses showed that only ECB140 possessed a complete route for L-tryptophan synthesis among all 15 strains. High-performance liquid chromatography and qRT-PCR confirmed the capability of ECB140 to produce L-tryptophan. Besides, the genome also contains the biosynthesis pathways of several other essential amino acids, such as phenylalanine, threonine, valine, leucine, isoleucine and lysine. These results indicate that ECB140 has the ability to survive passage through the gut and could act as a candidate probiotic. The study describes a novel, natural silkworm gut symbiont capable of producing L-tryptophan. Enterococcus casseliflavus ECB140 physical and genomic attributes offer possibilities for its colonization and provide L-tryptophan for lepidopteran insects.

Effects of pesticide application and plant sexual identity on leaf physiological traits and phyllosphere bacterial communities

AbstractPesticides are widely used to enhance food production on a global scale. However, little information is available on the effects of pesticide application on leaf physiology and phyllosphere bacterial communities of dioecious plants. Therefore, this study aimed to assess the impact of λ-cyhalothrin, a broad-spectrum pesticide, on leaf physiology and phyllosphere bacterial communities in the dioecious Populus cathayana. Physiological leaf traits such as photosynthetic apparatus (net photosynthetic rate (Pn), stomatal conductance (gs) and transpiration (E)) of males were significantly higher than those of females, independent of pesticide use. In contrast, pesticide application significantly reduced the photosynthetic apparatus for both sexes, and the reduction was greater in males relative to females. Also, pesticide application significantly increased peroxidase (POD) activity and malondialdehyde (MDA) content and maintained superoxide dismutase (SOD) activity and total chlorophyll content in leaves of males. The phyllosphere bacteria showed some conserved characteristics, in which, Simpson and Shannon diversity indices were not affected by sex or pesticide application. Phyllosphere bacterial community composition differed between females and males, indicating that intrinsic sex significantly shapes the phyllosphere bacterial community. However, pesticide application significantly increased the relative abundance of Actinobacteria but reduced the relative abundance of Proteobacteria. Principal component analysis showed associations between leaf physiology and specific bacterial taxa. For instance, Proteobacteria negatively correlated with leaf SOD activity and MDA content, while Actinobacteria showed an opposite pattern. Our study highlights sex-specific phyllosphere bacterial community composition and leaf physiological traits in dioecious plants.

Linking soil bacterial community assembly with the composition of organic carbon during forest succession

Changes in the composition of organic carbon lead to shifts in the selective environment, which in turn contribute to changes in the composition and assembly process of soil bacterial communities at different successional stages. Deterministic and stochastic processes are expected to clarify bacterial community assembly process during long-term ecosystem recovery. Therefore, by studying the bacterial community of the organic horizon and mineral horizon during forest succession, the main role of organic carbon composition in determining soil bacterial community structure and assembly process during forest succession in the arid regions of Loess Plateau, China was revealed. Stochastic assembly was predominant in the organic horizon (75.0%) and mineral horizon (71.6%), and its relative contribution of stochastic assembly was similar in two horizons. In addition, network analyses demonstrated that bacterial nodes (as individual taxa) and connectivity between them was higher in the organic horizon (nodes: 297 and edges: 5242) than mineral horizon (nodes: 251 and edges: 1694). During forest succession, the bacterial community gradually changed to a K-strategy, and the degree of bacterial network connection cross the organic horizon and mineral horizon gradually decreased. The taxon- organic carbon composition cooccurrence network aided in identifying the relationship between the composition of organic carbon and the bacterial community, and ploysaccharide, methyl and aliphatic carbon were the main reason for the differences in the bacterial community. Meanwhile, the relationship between the composition of organic carbon in bacterial assembly was different in the organic horizon and mineral horizon: ploysaccharide, methyl, aliphatic, aromatics and carboxylic carbon were the main factors driving bacterial assembly in the organic horizon, whereas the interaction of them with bacterial traits jointly participated the assembly process in the mineral horizon. Our results highlight the importance of resource availability, particularly the composition of organic carbon, in determining how the microbial community composition assembles during forest succession.

Host control and the evolution of cooperation in host microbiomes

Humans, and many other species, are host to diverse symbionts. It is often suggested that the mutual benefits of host-microbe relationships can alone explain cooperative evolution. Here, we evaluate this hypothesis with evolutionary modelling. Our model predicts that mutual benefits are insufficient to drive cooperation in systems like the human microbiome, because of competition between symbionts. However, cooperation can emerge if hosts can exert control over symbionts, so long as there are constraints that limit symbiont counter evolution. We test our model with genomic data of two bacterial traits monitored by animal immune systems. In both cases, bacteria have evolved as predicted under host control, tending to lose flagella and maintain butyrate production when host-associated. Moreover, an analysis of bacteria that retain flagella supports the evolution of host control, via toll-like receptor 5, which limits symbiont counter evolution. Our work puts host control mechanisms, including the immune system, at the centre of microbiome evolution.

Genomic identification and phenotypic evaluation of yield traits and bacterial wilt resistance in high oleic peanut breeding lines developed by marker assisted backcrossing

The peanut rich in oleic acid in seed oil, also known as high oleic peanut, renders its products superior in human healthy diet, long shelf life and high oxidative stability in food and oil processing. High oleic peanut varieties in China are derived from a handful of high oleic donors with limited genetic background. Improvement of high oleic peanut cultivars by integrating key target traits is crucial for both food security and germplasm enhancement. Several superior high oleic peanut lines have been developed by marker assisted backcrossing in our breeding program. The objective of present study is to characterize bacterial wilt disease resistance and yield related traits in these novel peanut lines. The two-year disease nursery survival rates were used as an indicator for bacterial wilt resistance, and the diagnostic markers identified by QTL mapping were used for molecular verification. Genetic background of high oleic peanut lines was estimated by 40 K genotyping by target sequencing (GBTS) SNP panel. Preliminary and regional yield tests were performed for selected breeding lines in 2021. As a result, an elite high oleic peanut accession Yuhua183 was identified, inheriting the superior characteristics of its recurrent parent such as resistance to bacterial wilt, high shelling percentage and early maturity. The development of Yuhua183 broadened the genetic background of high oleic peanut germplasm, providing valuable genetic resources for peanut breeding and further utilization.

Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization

SummaryBacillus subtilis is known to promote plant growth and protect plants against disease. B. subtilis rapidly adapts to Arabidopsis thaliana root colonization, as evidenced by improved root colonizers already after 12 consecutive transfers between seedlings in a hydroponic setup. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits, in accordance with evolved isolates displaying increased root colonization associated with robust biofilm formation in response to the plant polysaccharide xylan and impaired motility. Interestingly, evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by an evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings highlight how a plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.

A Resistome Roadmap: From the Human Body to Pristine Environments

A comprehensive characterization of the human body resistome [sets of antibiotic resistance genes (ARGs)] is yet to be done and paramount for addressing the antibiotic microbial resistance threat. Here, we study the resistome of 771 samples from five major body parts (skin, nares, vagina, gut, and oral cavity) of healthy subjects from the Human Microbiome Project (HMP) and addressed the potential dispersion of ARGs in pristine environments. A total of 28,714 ARGs belonging to 235 different ARG types were found in the HMP proteome dataset (n = 9.1 × 107 proteins analyzed). Our study reveals a distinct resistome profile (ARG type and abundance) between body sites and high interindividual variability. Nares had the highest ARG load (≈5.4 genes/genome) followed by the oral cavity, whereas the gut showed one of the highest ARG richness (shared with nares) but the lowest abundance (≈1.3 genes/genome). The fluroquinolone resistance genes were the most abundant in the human body, followed by macrolide–lincosamide–streptogramin (MLS) or tetracycline. Most ARGs belonged to common bacterial commensals and multidrug resistance trait were predominant in the nares and vagina. Many ARGs detected here were considered as low risk for human health, whereas only a few of them, such as BlaZ, dfrA14, dfrA17, or tetM, were classified as high-risk ARG. Our data also provide hope, since the spread of common ARG from the human body to pristine environments (n = 271 samples; 77 Gb of sequencing data and 2.1 × 108 proteins analyzed) thus far remains very unlikely (only one case found in an autochthonous bacterium from a pristine environment). These findings broaden our understanding of ARG in the context of the human microbiome and the One-Health Initiative of WHO uniting human host–microbes and environments as a whole.

Copiotrophic Bacterial Traits Increase With Burn Severity One Year After a Wildfire

Wildfire and burn severity influence soil microbial communities during post-fire recovery. If post-fire differences in microbial communities affect soil carbon (C) pool dynamics, altered microbial communities could influence the transition of forests from C sources to C sinks during ecosystem recovery. For example, fire may change the abundance of copiotrophic and oligotrophic bacteria, influencing the kinetic rates of soil C pools due to differences in C-acquisition strategies and nutrient requirements. We assessed differences in soil bacterial communities and soil C pool kinetics 1 year after a wildfire in a mixed-conifer forest in northern California, United States. We determined whether differences in bacterial communities and soil C pools were related to copiotrophic versus oligotrophic life history strategies. Specifically, we assessed bacterial community oligotrophy versus copiotrophy based on phyla relative abundances and predicted 16S gene copy numbers. We then determined whether these life-histories were correlated with C pool kinetic rates. We further determined whether C degradation metabolic pathways predicted using PICRUSt2 were related to C pool kinetics. We found that copiotrophic bacteria exhibited greater abundance in burned areas than unburned areas, evidenced by increases in 16S rRNA gene copy number and by taxonomic classifications. Furthermore, the abundance of predicted metabolic pathways associated with fast-cycling C compounds increased with severity, including carbohydrate, alcohol, and amine degradation pathways, suggesting increased copiotrophic metabolic strategies. In contrast, the abundance of metabolic pathways of slow-cycling aromatic C compounds did not change, indicating oligotrophic metabolic strategies did not increase. The kinetic rate of the active C pool was positively related to the copiotrophic metabolic pathway of alcohol degradation, and negatively related to oligotrophic pathways like aromatic compound degradation. The links between C pool kinetics and phylum-level life-strategy classifications were ambiguous. Overall, our results suggest that metabolic life-strategies are related to soil C pool kinetics and could have short- and long-term impacts on soil C persistence during post-fire recovery. In the short-term, increased copiotrophy could increase soil C effluxviarapid cycling of labile C pools. However, over the longer-term lower prevalence of oligotrophic strategies could allow aromatic compounds associated with pyrogenic C to accumulate, increasing stable soil C stocks.

Patatin-like phospholipase CapV in Escherichia coli - morphological and physiological effects of one amino acid substitution

In rod-shaped bacteria, morphological plasticity occurs in response to stress, which blocks cell division to promote filamentation. We demonstrate here that overexpression of the patatin-like phospholipase variant CapVQ329R, but not CapV, causes pronounced sulA-independent pyridoxine-inhibited cell filamentation in the Escherichia coli K-12-derivative MG1655 associated with restriction of flagella production and swimming motility. Conserved amino acids in canonical patatin-like phospholipase A motifs, but not the nucleophilic serine, are required to mediate CapVQ329R phenotypes. Furthermore, CapVQ329R production substantially alters the lipidome and colony morphotype including rdar biofilm formation with modulation of the production of the biofilm activator CsgD, and affects additional bacterial traits such as the efficiency of phage infection and antimicrobial susceptibility. Moreover, genetically diverse commensal and pathogenic E. coli strains and Salmonella typhimurium responded with cell filamentation and modulation in colony morphotype formation to CapVQ329R expression. In conclusion, this work identifies the CapV variant CapVQ329R as a pleiotropic regulator, emphasizes a scaffold function for patatin-like phospholipases, and highlights the impact of the substitution of a single conserved amino acid for protein functionality and alteration of host physiology.

Genetics of tolerance to bacterial wilt disease in eggplant

ABSTRACT Understanding the inheritance pattern of bacterial wilt (BW) disease tolerance is important to maximize genetic potential in eggplant (Solanum melongena L.). The study was conducted employing populations P1, P2, F1, F2, BC1, and BC2 of the crosses ‘Utkal Anushree × Bidhan Suphala,’ ‘Utkal Anushree × Garia,’ and ‘Utkal Madhuri × Bidhan Super’ to understand genetic control of BW disease tolerance. The inheritance study indicated that tolerance to BW disease was conditioned by a single dominant gene in 3 Tolerant × Susceptible crosses. The nature, and magnitude, of gene action controlling inheritance of bacterial wilt-related traits (days to 1st appearance of BW disease and disease incidence of BW) differed between crosses and traits, mostly conditioned by nonadditive gene action and duplicate epistasis. The disparity between results from the chi-square goodness of fit test and other quantitative methods indicated that the chi-square goodness of fit test alone could be misleading in the study of genetic control of bacterial wilt related traits due to its subjectivity. Complementary epitasis in 2 crosses for days to 1st appearance of BW disease would be helpful in improvement of this trait through backcrossing. Duplicate epistasis controlling BW disease incidence suggested selection of desirable recombinants from the segregating population developed from bi-parental mating. The BW-tolerant plants, with an acceptable fruit weight, can be isolated from segregating generations with involvement of susceptible plants having a higher fruit weight.

Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley.

Continuous cropping often leads to an unbalanced soil microbial community, which in turn negatively affects soil functions. However, systematic research of how these effects impact the bacterial composition, microbial functional traits, and soil metabolites is lacking. In the present study, the rhizosphere soil samples of Tibetan barley continuously monocropped for 2 (CCY02), 5 (CCY05), and 10 (CCY10) years were collected. By utilizing 16S high-throughput sequencing, untargeted metabolomes, and quantitative microbial element cycling smart chips, we examined the bacterial community structure, soil metabolites, and bacterial functional gene abundances, respectively. We found that bacterial richness (based on Chao1 and Phylogenetic Diversity [PD] indices) was significantly higher in CCY02 and CCY10 than in CCY05. As per principal component analysis (PCA), samples from the continuous monocropping year tended to share more similar species compositions and soil metabolites, and exhibited distinct patterns over time. The results of the Procrustes analysis indicated that alterations in the soil metabolic profiles and bacterial functional genes after long-term continuous cropping were mainly mediated by soil microbial communities (P < 0.05). Moreover, 14 genera mainly contributed to the sample dissimilarities. Of these, five genera were identified as the dominant shared taxa, including Blastococcus, Nocardioides, Sphingomonas, Bacillus, and Solirubrobacter. The continuous cropping of Tibetan barley significantly increased the abundances of genes related to C-degradation (F = 9.25, P = 0.01) and P-cycling (F = 5.35, P = 0.03). N-cycling significantly negatively correlated with bacterial diversity (r = − 0.71, P = 0.01). The co-occurrence network analysis revealed that nine hub genera correlated with most of the functional genes and a hub taxon, Desulfuromonadales, mainly co-occurred with the metabolites via both negative and positive correlations. Collectively, our findings indicated that continuous cropping significantly altered the bacterial community structure, functioning of rhizosphere soils, and soil metabolites, thereby providing a comprehensive understanding of the effects of the long-term continuous cropping of Tibetan barley.

Characteristics of intestinal microbiota in male morphotypes of the giant freshwater prawn Macrobrachium rosenbergii

There is a close correlation between intestinal microbiota and development. However, our understanding of the relationship between the intestinal microbial community and phenotypic traits in giant freshwater prawn (GFP), Macrobrachium rosenbergii, remains limited. Here, we explored this association between the gut bacterial community composition and phenotypic traits of male morphotypes of the GFP by using culture-dependent and high-throughput sequencing approaches. The results showed that Lactococcus garvieae was the dominant bacterial species, and accounted for 83.3%, 82.7%, 65.5%, and 40.8% of the total bacteria in the orange claw (OC), small males (SM), blue claw (BC), and old blue claw (OBC) groups, respectively. The relative abundance of the intestinal bacterial communities in the OBC and SM groups differed significantly from that in the OC and BC groups. We also observed statistically significant associations between gut microbiota and phenotypic traits. Moreover, the results obtained by using the conventional culture method further confirmed that L. garvieae was significantly predominant in all groups and more abundant in the OC and BC groups, suggesting an important role of L. garvieae in GFP development. This finding strongly suggests that the intestinal microbiota of GFP is tightly correlated with the morphotypic differentiation likely owing to its effects on nutrient metabolism in the gut.

A comparative whole-genome approach identifies bacterial traits for marine microbial interactions

Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3–8%) and different B vitamins (57–70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.

Usability of bacteriological milk analyses for genetic improvement of udder health in Austrian Fleckvieh cows

In addition to somatic cell count records and clinical mastitis diagnoses, results of bacteriological milk analyses provide valuable information regarding udder health. The pathogen causing an udder infection is currently not considered in Austria as part of the information used for estimation of routine breeding values for mastitis resistance. Therefore the objective of this study was to estimate heritabilities for, and genetic correlations between, udder traits of bacterial infection (bacterial infection, gram-positive and gram-negative bacterial infection) and routinely recorded udder health traits [acute mastitis, chronic mastitis, culling due to udder health problems, and somatic cell score (SCS)] in Austrian Fleckvieh cows. The basis for the genetic analyses was a data set with results from bacteriological milk analyses collected from 237 dairy farms and 6,822 cows over a period of 1 yr. Traits were defined as binary, apart from SCS, for which measures were available continuously. Multivariate analyses using a linear animal model were applied for estimating genetic parameters. The heritabilities for the occurrence of bacterial udder infection traits were 0.01. Heritabilities were 0.04 for acute mastitis, 0.02 for chronic mastitis, 0.02 for culling due to udder health problems, and 0.20 for SCS. Genetic correlations between bacteriological infection and the routinely recorded udder health traits were positive and ranged from 0.62 to 0.96. The genetic correlation between gram-positive and gram-negative bacterial infection was -0.20. The genetic correlation between acute and chronic mastitis was also close to zero. These results show that mastitis caused by different pathogens may be seen as different traits. As analyses were based on a relatively small data set and results were associated with rather high standard errors, further research with a larger data set should be carried out to confirm these results.