Phylum Actinobacteria Research Articles

The Science Underlying the Probiotic Strain Bifidobacterium in Beneficial Effects on Immunological and Gastrointestinal Health

Probiotics have demonstrated a lot of promise in improving gut health in humans. Despite the encouraging data, nothing is known about the therapeutic effectiveness of many of the probiotics on the market, and it's sometimes unclear how they work. Humans have long used Bifidobacterium, a well-known, multifunctional probiotic, to treat gastrointestinal, immunological, and infectious disorders. It is also therapeutically useful. This review provides a theoretical framework for comprehending the mechanisms of action of Bifidobacterium and highlights the functional advantages from the most pertinent animal and clinical trials. The genus Bifidobacterium belongs to the Actinobacteria phylum. = Firmicutes, Bacteroidetes, and Actinobacteria constitute the most abundant phyla in the human intestinal microbiota, Firmicutes and Bacteroidetes being predominant in adults, and Actinobacteria in breast-fed infants, where bifidobacteria can reach levels higher than 90% of the total bacterial population. They are among the first microbial colonizers of the intestines of newborns, and play key roles in the development of their physiology, including maturation of the immune system and use of dietary components. Indeed, some nutrients, such as human milk oligosaccharides, are important drivers of bifidobacterial development. Some Bifidobacterium strains are considered probiotic microorganisms because of their beneficial effects, and they have been included as bioactive ingredients in functional foods, mainly dairy products, as well as in food supplements and pharma products, alone, or together with, other microbes or microbial substrates. Well-documented scientific evidence of their activities is currently available for bifidobacteria containing preparations in some intestinal and extraintestinal pathologies. In particular, it regulates luminal metabolism, maintains gut microbiota stability, and eventually promotes a precisely calibrated homeostatic equilibrium in the host-microbiome relationship. An ideal probiotic selection would benefit from clinical proof of the multifunctional activities' efficacy and mechanism of action.

Resistance of soil bacterial communities from montane heathland ecosystems in the Cantabrian mountains (NW Spain) to a gradient of experimental nitrogen deposition

Elevated atmospheric nitrogen (N) deposition on terrestrial ecosystems has become one of the most important drivers of microbial diversity loss on a global scale, and has been reported to alter the soil function of nutrient-poor, montane Calluna vulgaris heathlands in the context of global change. In this work we analyze for the first time the shifts of bacterial communities in response to experimental addition of N in Calluna heathlands as a simulation of atmospheric deposition. Specifically, we evaluated the effects of five N addition treatments (0, 10, 20, and 50 kg N ha−1 yr−1 for 3-years; and 56 kg N ha−1 yr−1 for 10-years) on the resistance of soil bacterial communities as determined by changes in their composition and alpha and beta diversities. The study was conducted in montane Calluna heathlands at different development stages (young and mature phases) in the southern side of the Cantabrian Mountains (NW Spain). Our results evidenced a substantial increase of long-term (10-years) N inputs on soil extractable N-NH4+, particularly in young Calluna stands. The alpha diversity of soil bacterial communities in mature Calluna stands did not show a significant response to experimental N addition, whereas it was significantly higher under long-term chronic N addition (56 kg N ha−1 yr−1 for 10-years) in young Calluna stands. These bacterial community shifts are mainly attributable to a decrease in the dominance of Acidobacteria phylum, the most representative in montane Calluna ecosystems, in favor of copiotrophic taxa such as Actinobacteria or Proteobacteria phyla, favored under increased N availability. Future research should investigate what specific ecosystem functions performed by soil bacterial communities may be sensitive to increased nitrogen depositions, which may have substantial implications for the understanding of montane Calluna ecosystems' stability.

Stool microbiota analysis for abundance of genus Klebsiella among adults and children in endemic area for community Klebsiella pneumoniae infection

BackgroundInvasive Klebsiella pneumoniae syndrome is a significant endemic disease in Taiwan. Intestinal colonization of virulent clones that cause this phenomenon has been demonstrated in asymptomatic adults. Comparisons of healthy adults and children with stool K. pneumoniae colonization have rarely been reported. We aimed to evaluate the frequency and abundance of K. pneumoniae in the stool of adults and children by stool microbiota analysis. MethodsHealthy volunteers and their children without antibiotic exposure within 3 months were recruited in a Taiwanese medical center. Stool samples were sent for gut microbiota analysis, using amplification of V3–V4 hypervariable regions of 16sRNA followed by high-throughput sequence. Rectal/stool swabs were sent for K. pneumoniae culture and identification by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). ResultsFifty-five adults with a mean age of 46.9 years (range, 23.1–72.1 years) and 20 children with a mean age of 2.3 years (range, 0.9–5.8) were enrolled, and 29 adults and 6 children had positive K. pneumoniae swabs. Children had lower microbiota diversity than adults, including higher abundance of phylum Actinobacteria and Proteobacteria, and lower Bacteriodetes. For genus comparison, higher abundance of Escherichia, Streptococcus, Enterococcus and Bifidobacterium were found in children, but the composite abundance of Klebsiella in adults (median: 0.0156, range: 0–0.031) and in children (median: 0.0067, range: 0–0.043) were similar. Klebsiella abundance was significantly higher in participants with positive swabs (p < 0.0001). Klebsiella-positive swabs were strongly negatively correlated with Enterobacter spp. (p < 0.0001), but no known demographic factors correlated with Klebsiella-positive swabs. ConclusionKlebsiella species are present in young children, and the abundance is similar in adults and children. Positive swabs correlate strongly with higher abundance in microbiota analysis.

Analysis of the Influence of Oil Pollution on the Bacterial Component of Groundwater in a Karst Region on the Territory of a Long-term Developed Oil Field

The influence of oil pollution of groundwater in a karst region onto the bacterial component was studied. It has been established that bacteria are present in groundwater in an amount of 103–106 cells/ml. Representatives of the genus Arthobacter, Microbacterium, Rhodococcus, Williamsia (phylum Actinobacteria), Achromobacter and Pseudomonas (phylum Proteobacteria), Bacillus and Brevibacteria (phylum Firmicutes) were revealed. The state of the microbial component of the studied groundwater was analyzed according to the scale of environmental modifications. It was concluded that, with the exception of the release of groundwater at a site 320 m away from the oil field facilities, bacteriocenoses are in a state of "anthropogenic ecological stress".

Effects of Mineral Chinese Medicine Chloriti Lapis on Gut Microbiota of Small Intestine in PTZ-kindling Epileptic Rats

Background: Epilepsy is a neurological disease, and its clinical treatment presents a significant medical challenge. Nevertheless, Chloriti Lapis (CL), a traditional Chinese Mineral Medicine, has been employed for centuries to address neurological disorders and has shown notable effectiveness. Objectives: The objectives of this study are to further explore whether CL can modulate the abundance and diversity of the small intestinal flora in rats with epilepsy induced by pentylenetetrazol (PTZ) and to investigate the interrelationship among the flora. Materials and Methods: Operational taxonomic units (OTUs), α diversity, β diversity, hierarchical clustering tree, and principal component analysis (PCA) were utilized to analyze the small intestinal flora of PTZ-kindled epileptic rats. Results: The predominant bacterial groups in the small intestine mainly belonged to the phyla Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes. The administration of CL was found to effectively increase the abundance and diversity of the small intestinal flora, modify its structural composition, reduce the relative abundance of PTZ-elevated microflora, and enhance the abundance of Streptococcus, Staphylococcus, and Gemella Berger. Conclusion: CL exhibits promising potential, reliability, and unique value in managing epilepsy through the regulation of intestinal flora.

Efficacy and Skin Microbiome Modulation Effects of a Fixed-Concentration Combination of Benzoyl Peroxide 4% Plus Niacinamide 4% in a Film-Forming Cream in Subjects with Mild-to-Moderate Acne: A Non-Sponsored, Prospective, Assessor-Blinded, Pilot Trial

Benzoyl peroxide (BPO) and niacinamide (Niac) are commonly used alone or in combination with other molecules in the treatment of acne. BPO and Niac in the same product could exert complementary and synergistic effects improving efficacy in acne. Furthermore, Niac could reduce some side effects of BPO, such as skin irritation and erythema. A film-forming cream product containing BPO 4% and Niac 4%, vehiculated in a mixture of polyvinyl alcohol (PVA) and perfluoropolyether (PFPE) has been recently developed (B-N cream). A 28-day, assessor-blinded pilot trial was conducted to evaluate the clinical efficacy, skin tolerability, sebum production, skin redness, and skin microbiome modulation of B-N cream in subjects with mild to moderate acne of the face. Twenty-two adult men and women with mild-to-moderate acne of the face participated in this trial, after their written informed consent. B-N cream was applied once daily in the evening. The use of B-N cream was associated with a statistically significant decrease in acne lesions after treatment in comparison with baseline (non-inflammatory lesions: −40%; inflammatory lesions: −43% and total lesions: −41%). The use of the cream was not associated with a skin barrier function alteration. The skin redness score (−11%) and the sebum production (−42%) were significantly reduced after treatment. The use of B-N cream determined a reduction in the relative abundance of the Actinobacteria phylum (Corynebacterium and Propionibacterium, from 56% to 47%) and a significant increase in the abundance of Bacteroidetes phylum (from 3% to 5.2%). In addition, the product was well tolerated. In conclusion, this film-forming, medical device cream was effective in subjects with mild-to-moderate acne, reducing acne lesions and sebum production without altering skin barrier function, offering good skin tolerability. Furthermore, this product exerts positive skin microbiome modulation effects.

Red meat intake, faecal microbiome, serum trimethylamine N-oxide and hepatic steatosis among Chinese adults.

Emerging evidence suggests a detrimental impact of high red meat intake on hepatic steatosis. We investigated the potential interplay between red meat intake and gut microbiome on circulating levels of trimethylamine N-oxide (TMAO) and hepatic steatosis risk. This cross-sectional study was conducted in a representative sample of 754 community-dwelling adults in Huoshan, China. Diet was collected using 4 quarterly 3 consecutive 24-h dietary (12-day) recalls. We profiled faecal microbiome using 16S ribosomal RNA sequencing and quantified serum TMAO and its precursors using LC-tandem MS (n = 333). We detected hepatic steatosis by FibroScan. The adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were calculated using logistic regression. TMAO levels but not its precursors were positively associated with the likelihood of hepatic steatosis (aOR per 1-SD increment 1.86, 95% CI 1.04-3.32). We identified 14 bacterial genera whose abundance was associated with TMAO concentration (pFDR < .05) belonging to the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria families. Per 10 g/day increase in red meat intake was positively associated with TMAO levels among participants who had higher red meat intake (>70 g/day) and higher TMAO-predicting microbial scores (TMS, β = .045, p = .034), but not among others (pinteraction = .030). TMS significantly modified the positive association between red meat and steatosis (pinteraction = .032), with a stronger association being observed among participants with higher TMS (aOR 1.30, 95% CI 1.07-1.57). The bacterial genera that predicted TMAO levels may jointly modify the association between red meat intake and TMAO levels and the subsequent risk of hepatic steatosis.

Gut-Lung Microbiota Characterization in Patients with Non-Small Cell Lung Carcinoma and COVID-19 Coinfection.

Non-small cell lung cancer (NSCLC) patients with COVID-19 have an excessive chance of morbidity and mortality. The fecal-nasopharyngeal microbiota compositions of NSCLC patients were assessed in this study. In total, 234 samples were collected from 17 NSCLC patients infected with COVID-19, 20 NSCLC patients without confirmed COVID-19, 40 non NSCLC patients with COVID-19, and 40 healthy individuals. In lung microbiota, the abundance of Streptococcus spp. in NSCLC patients with confirmed COVID-19 was significantly higher than the two control groups. Pseudomonas aeruginosa and Staphylococcus aureus were listed as the most frequent pulmonary bacterial groups that colonized COVID-19 patients. In fecal specimens, the numbers of Bacteroidetes, Firmicutes, and Actinobacteria phyla were significantly higher amongst NSCLC patients with COVID-19. NSCLC patients infected with COVID-19 showed lower levels of Lactobacillus spp., Akkermansia muciniphila, and Bifidobacterium spp. The counts of Streptococcus spp., in NSCLC patients with COVID-19 were significantly higher than those of healthy individuals (8.49±0.70 log CFU/g wet feces vs 8.49±0.70 log CFU/g wet feces). Prevotella spp. were enriched in the gut and respiratory tracts of COVID-19 patient groups. The unbiased analysis showed an increment in Enterococcus spp., Streptococcus spp., and Prevotella spp. Eventually, it was found that compared to control groups, COVID-19 patients with NSCLC showed diminished gut bacteria diversity and increase in Lactobacillus spp., A. muciniphila, and Bifidobacterium spp. The overgrowth of Enterococcus spp., Streptococcus spp., and Prevotella spp. could be potential predictive biomarkers in the gut-lung axis of NSCLC patients with COVID-19.

Gut bacteriome in inflammatory bowel disease: An update on recent advances.

Inflammatory bowel diseases (IBD) are chronic inflammatory gut disorders, majorly classified as ulcerative colitis and Crohn's disease. The complex, multifactorial etiopathogenesis of IBD involves genetic predisposition, environmental cues, aberrant mucosal immune response and a disturbed gut microbiota. Epidemiological trends, studies in gnotobiotic mice models and genome-wide association studies, identifying genes involved in microbial handling, together mount evidence in support of the gut microbiota playing a pivotal role in IBD pathogenesis. Both Crohn's disease and ulcerative colitis are characterized by severe dysbiosis of the gut microbiome, marked by an expansion of detrimental taxa and concomitant depletion of beneficial members. IBD is characterized by reduction in abundances of bacterial genera involved in production of short-chain fatty acids, bio-transformations of bile acids and synthesis of indole-based tryptophan compounds such as Faecalibacterium, Ruminococcus, Coprococcus, Dorea, Parabacteroides, Eubacterium, Oscillibacter and Prevotella and elevation in members of phyla Proteobacteria and Actinobacteria. This imbalance not only results in exaggerated immune signaling towards the microbial antigens, but also results in an altered metabolomic milieu that triggers additional inflammatory cascades. The present review provides insights into the bacterial dysbiosis observed across different intestinal sites and their metabolomic imprints participating in IBD.

Abstract A016: The breast cancer genome and its association with the breast tissue bacteriome

Abstract BC is the most prevalent and leading fatal cancer type in women, yet the causes of most cases are unknown, indicating the necessity of deciphering contributing factors to quicken detection and inform therapeutic options. This research explores the relationship between the breast cancer (BC) genome and breast tissue bacteriome. BC forms in microenvironments in which genes and bacteria are in close proximity and research evidences gene-bacteria communication, but the relationship between the BC genome and the changing breast tissue bacteriome is not well understood. We hypothesized that genetic variation in the top ten genes commonly linked to BC: BRCA1, BRCA2, PTEN, TP53, PALB2, CHEK2, ATM, BRIP1, BARD1 , and STK11 would be associated with variations in the breast tissue bacteriome. We conducted 30X whole genome sequencing on 60 breast tissue samples (healthy, H (n=15), pre-diagnostic, PD (n=15), tumor, T (n=15), and adjacent normal, AN (n=15)) donated to the Susan G. Komen and Indiana University Simon Cancer Center Tissue Banks. These same samples were previously analyzed for microbiome composition and function using 16S rRNA sequencing (published in mSystems, 2022). Following sequence pre-processing, variant calling, and alternate allele frequency calculation by the UC Davis Bioinformatics Core, we selected only high and moderate variants for these genes with a quality score ≥ 55 for further analysis. Of the ten we intended to analyze, only 8 met these criteria within our data set: BRCA1, BRCA2, PTEN, TP53, PALB2, CHEK2, ATM , and BRIP1 . We ran generalized linear models to select variants with differences in alternate allele frequency among the tissue types (H, PD, AN, T, p ≤ 0.2). Alternate allele frequencies and genotypes of these variants that passed this filter were then associated with bacterial ASVs deemed differentially abundant relative to the H tissue type (mSystems, 2022) using MaAsLin2. Three BC-linked genes BRCA1, TP53 , and ATM show significant associations with the taxa, Muribaculaceae, Alcaligenes faecalis, Oceanobacillus, Romboutsia, Pseudomonas , and Pseudomonas fragi , at a p-value ≤ 0.01 and q-value ≤ 0.25. These genera belong to phyla (Bacteroides, Firmicutes, and Actinobacteria) which have been shown to either interact directly with the genome to produce cancer-causing DNA damage, or to be associated with other types of cancer, suggesting their likely role in tumorigenesis. The discovered associations further our understanding of the genetic and microbial determinants of breast cancer and may highlight the breast tissue bacteriome as a biomarker of BC. Citation Format: Ariana McCaw, Rachel Jiang, Lindsey Marian, Leah Stiemsma. The breast cancer genome and its association with the breast tissue bacteriome [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A016.

Diversity, Composition, and Specificity of the Philaenus spumarius Bacteriome.

Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae) was recently classified as a pest due to its ability to act as a vector of the phytopathogen Xylella fastidiosa. This insect has been reported to harbour several symbiotic bacteria that play essential roles in P. spumarius health and fitness. However, the factors driving bacterial assemblages remain largely unexplored. Here, the bacteriome associated with different organs (head, abdomen, and genitalia) of males and females of P. spumarius was characterized using culturally dependent and independent methods and compared in terms of diversity and composition. The bacteriome of P. spumarius is enriched in Proteobacteria, Bacteroidota, and Actinobacteria phyla, as well as in Candidatus Sulcia and Cutibacterium genera. The most frequent isolates were Curtobacterium, Pseudomonas, and Rhizobiaceae sp.1. Males display a more diverse bacterial community than females, but no differences in diversity were found in distinct organs. However, the organ shapes the bacteriome structure more than sex, with the Microbacteriaceae family revealing a high level of organ specificity and the Blattabacteriaceae family showing a high level of sex specificity. Several symbiotic bacterial genera were identified in P. spumarius for the first time, including Rhodococcus, Citrobacter, Halomonas, Streptomyces, and Providencia. Differences in the bacterial composition within P. spumarius organs and sexes suggest an adaptation of bacteria to particular insect tissues, potentially shaped by their significance in the life and overall fitness of P. spumarius. Although more research on the bacteria of P. spumarius interactions is needed, such knowledge could help to develop specific bacterial-based insect management strategies.

Gut Microbiota Profile of Infants with Breastfeeding and Mixed Feeding Patterns

We explore the gut microbiota profiles of 103 stool samples collected from infants at the age of 4 and 6 months in Jakarta, Indonesia. We performed 16S rRNA gene sequencing with Illumina MiSeq to identify the diversity, structure, and composition of the gut microbiota from those stool samples. Among 103 stool samples, 55 and 48 samples were collected from infants with breastfeeding and mixed feeding patterns, respectively. We found that the most abundant bacteria were Bifidobacteriales from the phylum of Actinobacteria (43.05%), Lactobacillales from the phylum of Firmicutes (28.39%), and Enterobacterales from the phylum of Proteobacteria (13.75%). The alpha and beta diversity analysis showed that the association between feeding patterns and differences in the microbial communities was not statistically significant (p-value &gt;0.05). Our study did not show a difference in the gut microbiota pattern between the two feeding pattern groups. This result contributed to the variety of the world gut microbiota profile data in infants.

P1210 Gut microbiota profiling and disease course in patients with ulcerative colitis in clinical remission

Abstract Background The inflammatory bowel diseases, encompassing ulcerative colitis (UC) and Crohn’s disease (CD) are characterized by a relapsing-remitting disease course. Despite achieving remission, approximately one-third of the patients relapse annually and yet the microbiota associated with relapse remains elusive. We hypothesized that distinctions in gut microbial composition among patients in clinical remission could potentially influence the disease course. We aimed to discern a distinctive microbial signature in patients with UC in clinical remission, which could serve as a predictive marker for the sustained clinical remission. Methods This was a prospective observational cohort study conducted as a collaborative work between Dayanand Medical College and Hospital (DMCH), Ludhiana, and Institute of Microbial Technology (IMTECH), Chandigarh. Adult (≥18 years age) patients with an established diagnosis of mild UC (defined as no previous requirement of immune-modulators or biologics to induce or maintain remission) and in clinical remission, were included between January 2019 and December 2020 and followed for one year. The clinical remission was defined as partial Mayo score &amp;lt;2 for at least 6 months, with endoscopic Mayo score 0 and fecal calprotectin &amp;lt;100 µg/g within 4 weeks of enrolment. Utilizing using 16S rRNA metabarcoding based metagenome analysis, the bacterial composition of the collected stool samples were determined. Results During the study period, 34 patients (mean age 41.41±13.89 years, 20 [58.82%] males) meeting the eligibility criteria were included for analysis and followed up for one year. (Figure 1) The majority of the patients (21, 61.76%) had left sided colitis. On follow-up, 14 patients (41.17%) experienced a disease relapse (median time to relapse 6 [3-8.25] months). The phyla Firmicutes, Actinobacteria, Bacteroidetes and Proteobacteria were abundant in both the groups [sustained remission (n=20) and disease relapse (n=14)], but specific phyla were enriched in each cohort, Actinobacteria in remission and Proteobacteria in relapse groups. The genera Escherichia, Klebsiella, Enterobacter, Enterococcus, Streptococcus were enriched in relapse group. Interestingly the genus Clostridium was enriched in relapsed cohort whereas genera like Bifidobacterium, Prevotella, Bacteroides, Alistipes, Faecalibacterium were abundant in the remission cohorts. Conclusion There are inter-individual differences in the gut microbiota profile of patients with UC in clinical remission. These microbial differences can serve as determinants of the disease course.

Investigation of potential rubber-degrading bacteria and genes involved.

COVID-19 pandemic has generated high demand for natural rubber gloves (NR) leading to crucial issues of rubber waste and waste management such as burning, dumping, stockpiling, discarding waste in landfills. Hence, rubber biodegradation by microorganisms is an alternative solution to the problem. The biodegradation method is environmentally friendly but normally extremely slow. Numerous microorganisms can degrade NR as a source of carbon and energy. In this study, Rhodococcus pyridinivorans KU1 was isolated from the consortium CK from previous study. The 40% rubber weight loss was detected after incubated for 2months. The bacterial colonization and cavities on the surface of rubber were identified using a scanning electron microscope (SEM). The result demonstrated the critical degradation of the rubber surface, indicating that bacteria can degrade rubber and use it as their sole carbon source. The result of whole-genome sequencing (WGS) revealed a gene that is 99.9% identical to lcp which is responsible for poly (cis-1,4-isoprene) degradation. The results from Meta16S rRNA sequencing showed that the microbial communities were slightly shifted during the 2-month degradation, depending on the presence of monomers or oligomers appeared during the degradation process. The majority of species were soil bacteria such as phylum Proteobacteria, Actinobacteria, and Firmicutes. Members of Pseudoxanthomonas seemed to be the dominant degraders throughout the degradation.

Skin Microbial Community Associated to Strawberry Disease in Farmed Rainbow Trout (Oncorhynchus mykiss Walbaum, 1792).

Aquaculture plays a crucial role in addressing the growing global demand for food. However, diseases associated with intensive aquaculture practices, especially those affecting the skin, can present significant challenges to both fish health and the industry as a whole. Strawberry disease (SD), also known as red-mark syndrome, is a persistent and non-lethal skin condition observed in Rainbow Trout (Oncorhynchus mykiss) in the United States and various European countries. SD is a nonlethal skin condition of an unclear etiology that affects rainbow trout reared in freshwater close to the harvest period. We used a RNA-based approach to examine active microbiota in the SD skin lesions and compared to non-injured skin. Our results, based on using 16S rRNA gene next-generation sequencing, showed that the skin microbiota was dominated by the phyla Firmicutes, Proteobacteria, and Actinobacteria. The comparisons of the skin microbiota between injured and non-injured samples showed differences in the alpha diversity (Fisher index) and beta diversity metrics (ANOSIM). At the genus level, both Pseudomonas and Candidatus Midichloria were highlighted as the most abundant taxa detected in samples obtained from fish affected with strawberry diseases. In contrast, the most abundant taxa in non-injured skin were Escherichia-Shigella, Streptococcus, and Pseudoalteromonas. In conclusion, our study on SD revealed distinct differences in the microbiota composition between skin lesions and non-injured skin. This is the first description of microbiota associated with SD-injured skin samples using an RNA approach.

The microbial community, nutrient supply and crop yields differ along a potassium fertilizer gradient under wheat–maize double-cropping systems

Soil microorganisms play critical roles in ecosystem function. However, the relative impact of the potassium (K) fertilizer gradient on the microbial community in wheat-maize double-cropping systems remains unclear. In this long-term field experiment (2008–2019), we researched bacterial and fungal diversity, composition, and community assemblage in the soil along a K fertilizer gradient in the wheat season (K0, no K fertilizer; K1, 45 kg ha−1 K2O; K2, 90 kg ha−1 K2O; K3, 135 kg ha−1 K2O) and in the maize season (K0, no K fertilizer; K1, 150 kg ha−1 K2O; K2, 300 kg ha−1 K2O; K3, 450 kg ha−1 K2O) using bacterial 16S rRNA and fungal internally transcribed spacer (ITS) data. We observed that environmental variables, such as mean annual soil temperature (MAT) and precipitation, available K, ammonium, nitrate, and organic matter, impacted the soil bacterial and fungal communities, and their impacts varied with fertilizer treatments and crop species. Furthermore, the relative abundance of bacteria involved in soil nutrient transformation (phylum Actinobacteria and class Alphaproteobacteria) in the wheat season was significantly increased compared to the maize season, and the optimal K fertilizer dosage (K2 treatment) boosted the relative bacterial abundance of soil nutrient transformation (genus Lactobacillus) and soil denitrification (phylum Proteobacteria) bacteria in the wheat season. The abundance of the soil bacterial community promoting root growth and nutrient absorption (genus Herbaspirillum) in the maize season was improved compared to the wheat season, and the K2 treatment enhanced the bacterial abundance of soil nutrient transformation (genus MND1) and soil nitrogen cycling (genus Nitrospira) genera in the maize season. The results indicated that the bacterial and fungal communities in the double-cropping system exhibited variable sensitivities and assembly mechanisms along a K fertilizer gradient, and microhabitats explained the largest amount of the variation in crop yields, and improved wheat-maize yields by 11.2–22.6 and 9.2–23.8% with K addition, respectively. These modes are shaped contemporaneously by the different meteorological factors and soil nutrient changes in the K fertilizer gradients.

Soybean microbiome composition and the impact of host plant resistance.

Microbial communities play an important role in the growth and development of plants, including plant immunity and the decomposition of complex substances into absorbable nutrients. Hence, utilizing beneficial microbes becomes a promising strategy for the optimization of plant growth. The objective of this research was to explore the root bacterial profile across different soybean genotypes and the change in the microbial community under soybean cyst nematode (SCN) infection in greenhouse conditions using 16S rRNA sequencing. Soybean genotypes with soybean cyst nematode (SCN) susceptible and resistant phenotypes were grown under field and greenhouse conditions. Bulked soil, rhizosphere, and root samples were collected from each replicate. Sequencing of the bacterial 16S gene indicated that the bacterial profile of soybean root and soil samples partially overlapped but also contained different communities. The bacterial phyla Proteobacteria, Actinobacteria, and Bacteroidetes dominate the soybean root-enriched microbiota. The structure of bacteria was significantly affected by sample year (field) or time point (greenhouse). In addition, the host genotype had a small but significant effect on the diversity of the root microbiome under SCN pressure in the greenhouse test. These differences may potentially represent beneficial bacteria or secondary effects related to SCN resistance.

Unraveling the role of bacterial communities in mangrove habitats under the urban influence, using a next-generation sequencing approach

Mangrove ecosystems are vital coastal habitats with rich biodiversity and play a significant role in carbon sequestration, these habitats are facing mounting threats from rapid urbanization. This study delves into assessing the sediment bacterial communities from the urban mangrove habitats of Campal and Panaji, within the Mandovi estuarine environment of Goa, to understand the intricate interplay between urbanization and bacterial dynamics in the mangrove habitats. We used a combined approach of 16S amplicon and shotgun sequencing methodologies to understand the bacterial taxonomic composition and functional profiles. The community structure revealed the dominance of bacterial groups from phylum Proteobacteria, Chloroflexi and Actinobacteria at both locations. The impact of urbanization was evident from the increased abundance of pathogenic groups at class and genus levels in this region. The core microbiome analysis showed the presence of Shewanella, Pseudomonas and Clostridium which are mostly pathogenic, anaerobic taxa Woeseia, Rheinheimera, like genera that are involved in the organic matter cycling and unclassified bacteria. Though increased pathogenic forms are reported, it is evident that the dominant taxa also included groups that contributed to the biogeochemical cycling of organic matter in sediment from these locations. Functional diversity elucidated through shotgun metagenomics analysis showcased the predominance of carbohydrate metabolism and the presence of glycoside hydrolases degrading plant-based starch, pectin and cellulosic organic matter. The occurrence of xenobiotic biodegradation pathways is an indication of the presence of xenobiotic degrading microbes as a natural means of degrading high amounts of pollutants at this location. Comparative analysis of the metagenomes from this study with similar earlier studies at Ribandar, Mandovi and Cortalim, Zuari mangrove habitats of Goa with varying pollution levels also reiterates the terrestrial influence on the microbial community in these habitats. It showed that Panaji and Campal locations had the presence of dominant pathogenic forms which was absent in the other two locations. The Ribandar and Coratlim location which is reported to have a comparatively lesser impact due to anthropogenic activity had an increased abundance of distinct genera which are predominant heterotrophic forms involved in remineralization and reduced levels of pathogens. Our findings highlight the profound influence of urbanization on the sediment mangrove bacterial communities and spotlight the resilience and adaptability of these microorganisms. This calls for immediate action and preventive measures to restore their functional potential in maintaining the health of these ecosystems amidst expanding urban landscapes.

The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety.

Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.

Assessment of nitrification process in a sequencing batch reactor: Modelling and genomic approach

Nitrification of ammoniacal nitrogen (N–NH4+) to nitrate (N–NO3-) was investigated in a lab-scale sequencing batch reactor (SBR) to evaluate its efficiency. During the nitrification process the removal of N–NH4+ reached 96%, resulting in 73% formation of N–NO3-. A lineal correlation (r2 = 0.9978) was obtained between the concentration of volatile suspended solids (VSS) and the maximal N–NO3- concentration at the end of each batch cycle under stationary state. The bacterial taxons in the initial inoculum were identified, revealing a complex diverse community mainly in the two major bacterial phyla Proteobacteria and Actinobacteria. The FAPROTAX algorithm predicted the presence in the inoculum of taxa involved in relevant processes of the nitrogen metabolism, highlighting the bacterial genera Nitrospira and Nitrosomonas that are both involved in the nitrification process. A kinetic model was formulated for predicting and validating the transformation of N–NH4+, N–NO2- and N–NO3- and the removal of organic and inorganic carbon (TOC and IC, respectively). The results showed how the increase in biomass concentration slowed down the transformation to oxidised forms of nitrogen and increased denitrification in the settling and filling stages under free aeration conditions.