Diversity Of Bacteria Research Articles

Remediation of isoproturon-contaminated soil by Sphingobium sp. strain YBL2: Bioaugmentation, detoxification and community structure

The widely used phenylurea herbicide isoproturon (IPU) and its residues can inhibit the growth of subsequently planted crops. However, reports on bioremediation of IPU-contaminated soil are scarce. In this study, Sphingobium sp. strain YBL2-gfp (a derivative of the IPU-degrading Sphingobium sp. strain YBL2 isolated by our lab) was constructed to bioremediate IPU-contaminated soil. In pot experiments, strain YBL2-gfp colonized the roots of wheat and eliminated IPU residues in the soil within 21 d, effectively alleviating its toxicity and restoring wheat growth. IPU treatment reduced the richness and diversity of soil bacteria, while inoculation YBL2-gfp mainly affected richness with less impact on diversity. The high concentrations of IPU and inoculation of YBL2-gfp alone reduced the soil microbial community connections, while bioaugmentation treatment enhanced the soil microbial community connections. Additionally, strain YBL2-gfp stimulated the metabolic capacity of the indigenous microbes, promoting the degradation of IPU and reducing the negative impact of high concentrations of IPU on microbial community. Taken together, this study offers relatively comprehensive insights into the practical application of bioaugmentation, demonstrating that strain YBL2 has the potential to remediate IPU-contaminated soils.

One-Year Monitoring of Prevalence and Diversity of Dairy Propionic Acid Bacteria in Raw Milk by Means of Culture-Dependent and Culture-Independent Methods.

Even low levels of dairy propionic acid bacteria (dPAB) can cause cheese defects, resulting in severe economic losses for the producers of selected raw milk cheeses. Therefore, routine quality control of raw cheese milk for dPAB contamination is essential if propionic acid fermentation is undesired. Although knowledge of dPAB contamination of raw milk is important to understand cheese spoilage, long-term dPAB screening data are outdated, and studies taking into account different farm management parameters and their potential influence on dPAB levels are scarce. This study aims to provide insight into the dPAB levels of raw milk over time, to identify farm management factors that potentially influence dPAB levels, and to compare a cultural yeast extract lactate agar (YELA) and lithium glycerol agar (LGA) and a culture-independent method (qPCR) for dPAB quantification with respect to their applicability in routine quality control for the dairy industry. For this purpose, bulk tank milk from 25 dairy farms was screened for dPAB contamination over a one-year period. We were able to identify significant differences in the dPAB contamination levels in raw milk depending on selected farm-specific factors and observed relationships between the different types of milking systems and dPAB contamination levels in raw milk. When dPAB were quantified by cultivation on YELA, strong overgrowth of commensal microbiota impeded counting. Therefore, we conclude that quantification on LGA or by qPCR is preferable. Both methods, colony counting on LGA as well as quantification of dPAB using qPCR, have advantages for the application in (routine) quality control of raw milk, one being low-tech and inexpensive, the other being fast and highly specific, but the detection of (low level) dPAB contamination in raw milk remains a challenge.

Vegetation restoration increased the diversity and network complexity of carbon-fixing functional bacteria in heavily eroded areas of southern China

Carbon-fixing bacteria are a key functional group in soil carbon fixation processes, but their relationship with soil multifunctionality during vegetation restoration in eroded areas remains unclear. This hinders our ability to assess the true impact of vegetation restoration on soil ecosystem services. Therefore, we studied the impacts of three vegetation communities (tree-shrub, tree-grass, and tree-shrub-grass) in the same small watershed in a severely eroded area in southern China on the community of carbon-fixing bacteria in the soil. Compared to eroded areas, vegetation restoration sites had more complex networks of carbon-fixing bacteria, more carbon-fixing bacterial taxa, and more associations among these bacteria. Particularly, in the tree-shrub communities, the Chao1 index, Shannon index, node number, and edge number increased significantly by 291.29%, 49.65%, 364.58%, and 530.89%, respectively. The vegetation community pattern shifted the dominant carbon-fixing bacteria in the eroded areas from Rhodovastum to Nocardia. In the tree-shrub, tree-grass, and tree-shrub-grass patterns, the relative abundance of Rhodovastum decreased by 90.11%, 96.76%, and 95.37%, respectively, compared to that in the control group (CK). This indicates that vegetation community patterns have the potential to shift the dominant carbon-fixing bacteria from strict autotrophs to facultative autotrophs. The changes in the characteristics of the carbon-fixing bacterial community are closely related to the changes in soil multifunctionality caused by vegetation restoration. These results demonstrate that vegetation communities have a significant positive impact on the soil carbon fixation capacity.

Insights into the seasonal changes in the taxonomic and functional diversity of bacteria in the eastern Arabian Sea: Shotgun metagenomics approach

The eastern Arabian Sea (EAS) is known for its unique oceanographic features such as the seasonal monsoonal winds, upwelling of nutrient-rich waters and a significant increase in primary productivity during the monsoon season. In this study, we utilised the shotgun metagenomics approach to determine the seasonal variations in bacterial taxonomic and functional profiles during the non-monsoon and monsoon seasons in the EAS. Significant seasonal variations in the bacterial community structure were observed at the phylum and genera levels. These findings also correspond with seasonal shifts in the functional profiles of the bacterial communities based on the variations of genes encoding enzymes associated with different metabolic pathways. Pronounced seasonal variation of bacterial taxa was evident with an increased abundance of Idiomarina, Marinobacter, Psychrobacter and Alteromonas of Proteobacteria, Bacillus and Staphylococcus of Firmicutes during the non-monsoon season. These taxa were linked to elevated nucleotide and amino acid biosynthesis, amino acid and lipid degradation. Conversely, during the monsoon, the taxa composition changed with Alteromonas, Candidatus Pelagibacter of Proteobacteria and Cyanobacteria Synechococcus; contributing largely to the amino acid and lipid biosynthesis, fermentation and inorganic nutrient metabolism which was evident from functional analysis. Regression analysis confirmed that increased seasonal primary productivity significantly influenced the abundance of genes associated with carbohydrate, protein and lipid metabolism. These highlight the pivotal role of seasonal changes in primary productivity in shaping the bacterial communities, their functional profiles and driving the biogeochemical cycling in the EAS.

Manipulating soil resource availability to alter microbial communities for weed management in agroecosystems

The growing resistance of weeds to herbicides demands innovative strategies that harness soil biology for effective weed control. We examined the use of carbon amendments to stimulate microbial immobilization of soil nitrogen for weed control. We hypothesized that increased carbon availability will stimulate soil microbial growth, leading to greater nitrogen immobilization, which consequently decreases plant-available nitrogen and suppresses the growth of nitrogen-responsive weed species. We buried 80 19-L pots in a research farm field and added sawdust and sucrose to soils as a high carbon treatment and used unamended soils as a control. We examined eight different weed species separately, and measured plant growth, soil carbon, available nitrate, microbial carbon and nitrogen, and microbial community composition after 11 weeks of treatment. The carbon amendments altered plant-microbial competition for nitrogen, resulting in reduced biomass for most weed species. The carbon-amended soils had higher microbial biomass carbon and nitrogen, slower nitrogen cycling, and less available soil nitrogen, indicating enhanced nitrogen immobilization. The carbon treatment altered the beta diversity of soil fungi and bacteria and reduced fungal alpha diversity estimated by the Shannon index. The study results indicate that high carbon substrates can be used to modify plant-microbial competition for soil nitrogen with important implications for developing sustainable weed management practices.

Combined effects of cadmium and simulated acid rain on soil microbial communities in the early cultivation of Populus beijingensis seedlings

The combined cadmium (Cd) and acid rain pollution poses a significant threat to the global ecological environment. Previous studies on the combined adverse effects have predominantly focused on the aboveground plant physiological responses, with limited reports on the microbial response in the rhizosphere soil. This study employed Populus beijingensis seedlings and potting experiments to simulate the impacts of combined mild acid rain (pH=4.5, MA) or highly strong acid rain (pH=3.0, HA), and soil Cd pollution on the composition and diversity of microbial communities, as well as the physiochemical properties in the rhizosphere soil. The results showed that Cd decreased the content of inorganic nitrogen, resulting in an overall decrease of 49.10 % and 46.67 % in ammonium nitrogen and nitrate nitrogen, respectively. Conversely, acid rain was found to elevate the content of total potassium and soil organic carbon by 4.68 %-6.18 % and 8.64–19.16 %, respectively. Additionally, simulated acid rain was observed to decrease the pH level by 0.29–0.35, while Cd increased the pH level by 0.11. Moreover, Cd alone reduced the rhizosphere bacterial diversity, however, when combined with acid rain, regardless of its intensity, Cd was observed to increase the diversity. Fungal diversity was not influenced by the acid rain, but Cd increased fungal diversity to some extend under HA as observed in bacterial diversity. In addition, composition of the rhizosphere bacterial community was primarily influenced by the inorganic nitrogen components, while the fungal community was driven mainly by soil pH. Furthermore, “Metabolism” was emerged as the most significant bacterial function, which was markedly affected by the combined pollution, while Cd pollution led to a shift from symbiotroph to other trophic types for fungi. These findings suggest that simulated acid rain has a mitigating effect on the diversity of rhizosphere bacteria affected by Cd pollution, and also alters the trophic type of these microorganisms. This can be attributed to the acid rain-induced direct acidic environment, as well as the indirect changes in the availability or sources of carbon, nitrogen, or potassium.

The diversity and risk of potential pathogenic bacteria on the surface of glaciers in the southeastern Tibetan Plateau

Glaciers, which constitute the world's largest global freshwater reservoir, are also natural microbial repositories. The frequent pandemic in recent years underscored the potential biosafety risks associated with the release of microorganisms from the accelerated melting of glaciers due to global warming. However, the characteristics of pathogenic microorganisms in glaciers are not well understood. The glacier surface is the primary area where glacier melting occurs that is often the main subject of research on the dynamics of pathogenic microbial communities in efforts to assess glacier biosafety risks and devise preventive measures. In this study, high-throughput sequencing and quantitative polymerase chain reaction methods were employed in analyses of the composition and quantities of potential pathogenic bacteria on the surfaces of glaciers in the southeastern Tibetan Plateau. The study identified 441 potential pathogenic species ranging from 215 to 4.39 × 1011 copies/g, with notable seasonal and environmental variations being found in the composition and quantity of potential pathogens. The highest level of diversity was observed in April and snow, while the highest quantities were observed in October and cryoconite. Host analysis revealed that >70 % of the species were pathogens affecting animals, with the highest proportion of zoonotic pathogens being observed in April. Analysis of aerosols and glacial meltwater dispersion suggested that these microbes originated from West Asia, primarily affecting the central and southern regions of China. Null model analysis indicated that the assembly of potential pathogenic microbial communities on glacier surfaces was largely governed by deterministic processes. In conclusion, potential pathogenic bacteria on glacier surfaces mainly originated from the snow and exhibited significant temporal and spatial variation patterns. These findings can be used to enhance researchers' ability to predict potential biosafety risks associated with pathogenic bacteria in glaciers and to prevent their negative impact on populations and ecological systems.

Soil bacterial activity and functional diversity as indicators of recultivation of alkaline settlements of a ‘Solvay’ process

PurposeMany industries continuously produce large volumes of alkaline residues. After recultivation, former landfills can be an important element providing ecosystem services in highly urbanised areas.Materials and methodsWe studied the relationship between vegetation and soil bacterial characteristics using Biolog® ECO plates on recultivated areas of the Solvay heaps, and participation of invasive species in plant community in progressive succession.Results and discussionBacterial activity and functional diversity indices were correlated with soil physicochemical properties (soil organic matter content, water holding capacity, total phosphorus content, and soil pH). Plots with a higher total number of vascular plant species, including forest floor species, and a higher Shannon–Wiener index of vegetation diversity H'plant, were characterised by a higher amino acid utilisation by soil bacteria. Soil bacteria CLPP (community-level physiological profiles) were most influenced by soil physical and chemical properties, but also by the proportion of invasive species in the total number of plant species. In conclusion, soil physical and chemical properties dominate vegetation characteristics in shaping the functional diversity of soil bacteria. Invasive species may be an influential component of ecosystems during spontaneous succession of degraded soils.

Hundreds of antimicrobial peptides create a selective barrier for insect gut symbionts

The spatial organization of gut microbiota is crucial for the functioning of the gut ecosystem, although the mechanisms that organize gut bacterial communities in microhabitats are only partially understood. The gut of the insect Riptortus pedestris has a characteristic microbiota biogeography with a multispecies community in the anterior midgut and a monospecific bacterial population in the posterior midgut. We show that the posterior midgut region produces massively hundreds of specific antimicrobial peptides (AMPs), the Crypt-specific Cysteine-Rich peptides (CCRs) that have membrane-damaging antimicrobial activity against diverse bacteria but posterior midgut symbionts have elevated resistance. We determined by transposon-sequencing the genetic repertoire in the symbiont Caballeronia insecticola to manage CCR stress, identifying different independent pathways, including AMP-resistance pathways unrelated to known membrane homeostasis functions as well as cell envelope functions. Mutants in the corresponding genes have reduced capacity to colonize the posterior midgut, demonstrating that CCRs create a selective barrier and resistance is crucial in gut symbionts. Moreover, once established in the gut, the bacteria differentiate into a CCR-sensitive state, suggesting a second function of the CCR peptide arsenal in protecting the gut epithelia or mediating metabolic exchanges between the host and the gut symbionts. Our study highlights the evolution of an extreme diverse AMP family that likely contributes to establish and control the gut microbiota.

Deterministic processes dominate microbial assembly mechanisms in the gut microbiota of cold-water fish between summer and winter.

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%; Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments.

Diversity and Phylogeny of Symbiotic Bacteria Nodulating Common Bean (Phaseolus vulgaris L.) in Côte d’Ivoire

Phaseolus vulgaris L. (common bean) is an agriculturally important legume that benefits from a symbiosis with bacteria belonging to the genus Rhizobium. Growing interest in the use of rhizobia as biofertilizers has led to the identification of a large number of rhizobia strains and studies of their diversity. Although much research has been carried out on rhizobia, there is little data on the diversity of rhizobia associated with common bean in Côte d'Ivoire. This study assessed the species diversity of common bean nodulating bacteria in ivorian soils. This diversity was assessed based on 16S rRNA gene sequencing. Ten high-performance bacterial isolates extracted from common bean nodules were used for genetic analysis. The 16S rRNA gene sequences of the native isolates were closely affiliated with members of the genera Rhizobium, Bradyrhizobium, Allorhizobium and Sinorhizobium demonstrating the presence of a diversity of native bean nodule bacteria. This study also reports for the first time the presence of Allorhizobium taibaishanense in common bean nodules. These results constitute an important step in the development of an effective microbial inoculum and sustainable food production.

Innovative Delivery System Combining CRISPR-Cas12f for Combatting Antimicrobial Resistance in Gram-Negative Bacteria.

Antimicrobial resistance poses a significant global challenge, demanding innovative approaches, such as the CRISPR-Cas-mediated resistance plasmid or gene-curing system, to effectively combat this urgent crisis. To enable successful curing of antimicrobial genes or plasmids through CRISPR-Cas technology, the development of an efficient broad-host-range delivery system is paramount. In this study, we have successfully designed and constructed a novel functional gene delivery plasmid, pQ-mini, utilizing the backbone of a broad-host-range Inc.Q plasmid. Moreover, we have integrated the CRISPR-Cas12f system into the pQ-mini plasmid to enable gene-curing in broad-host of bacteria. Our findings demonstrate that pQ-mini facilitates the highly efficient transfer of genetic elements to diverse bacteria, particularly in various species in the order of Enterobacterales, exhibiting a broader host range and superior conjugation efficiency compared to the commonly used pMB1-like plasmid. Notably, pQ-mini effectively delivers the CRISPR-Cas12f system to antimicrobial-resistant strains, resulting in remarkable curing efficiencies for plasmid-borne mcr-1 or blaKPC genes that are comparable to those achieved by the previously reported pCasCure system. In conclusion, our study successfully establishes and optimizes pQ-mini as a broad-host-range functional gene delivery vector. Furthermore, in combination with the CRISPR-Cas system, pQ-mini demonstrates its potential for broad-host delivery, highlighting its promising role as a novel antimicrobial tool against the growing threat of antimicrobial resistance.

Effects of glyphosate-based herbicide on gut microbes and hepatopancreatic metabolism in Pomacea canaliculata

Roundup®, a prominent glyphosate-based herbicide (GBH), holds a significant position in the global market. However, studies of its effects on aquatic invertebrates, including molluscs are limited. Pomacea canaliculata, a large freshwater snail naturally thrives in agricultural environments where GBH is extensively employed. Our investigation involved assessing the impact of two concentrations of GBH (at concentrations of 19.98 mg/L and 59.94 mg/L, corresponding to 6 mg/L and 18 mg/L glyphosate) during a 96 h exposure experiment on the intestinal bacterial composition and metabolites of P. canaliculata. Analysis of the 16 S rRNA gene demonstrated a notable reduction in the alpha diversity of intestinal bacteria due to GBH exposure. Higher GBH concentration caused a significant shift in the relative abundance of dominant bacteria, such as Bacteroides and Paludibacter. We employed widely-targeted metabolomics analysis to analyze alterations in the hepatopancreatic metabolic profile as a consequence of GBH exposure. The shifts in metabolites primarily affected lipid, amino acid, and glucose metabolism, resulting in compromised immune and adaptive capacities in P. canaliculata. These results suggested that exposure to varying GBH concentrations perpetuates adverse effects on intestinal and hepatopancreatic health of P. canaliculata. This study provides an understanding of the negative effects of GBH on P. canaliculata and may sheds light on its potential implications for other molluscs.

Effects of Different Proportions of Ammonium Sulfate Replacing Urea on Soil Nutrients and Rhizosphere Microbial Communities

In order to investigate the effects of ammonium sulfate, an industrial by-product, on soil nutrients and microbial community when applied in different proportions instead of using urea as nitrogen fertilizer, a pot corn experiment was conducted. A completely randomized block experimental design was used, with a total of five treatments:CK (no fertilization), U10S0 (100 % urea), U8S2 (80 % urea + 20 % ammonium sulfate), U6S4(60 % urea + 40 % ammonium sulfate), and U0S10 (100 % ammonium sulfate). The basic physical and chemical properties of soil and the dry weight of maize plants were determined by conventional methods, and microbial sequencing was performed using the Illumina NovaSeq platform. The experiment results showed that:① In each growth stage of maize, the pH of soil treated with fertilization (7.85-8.15) was decreased compared with that of CK (8.1-8.21), and the pH showed a decreasing trend with the increase in ammonium sulfate content. ② The soil available nitrogen content increased gradually with the increase in the ammonium sulfate ratio at each growth stage of maize. Compared with that in the CK and U10S0 treatments, the ratio in the U0S10 treatment increased 30.56 % to 63.68 % and 13.22 % to 38.43 %, respectively. The variation trend of organic carbon content was opposite to that of available nitrogen (U8S2 > U6S4 > U0S10), and the addition of ammonium sulfate was still higher than that of U10S0 at other growth stages except for the seedling stage. ③ The protease activity of all fertilization treatments was higher than that of the control, and the protease activity was gradually enhanced with the continuous growth of corn and the increase in the ammonium sulfate ratio. The protease activity of the U0S10 treatment was higher than that of the U10S0 treatment at each growth stage of corn, which increased by 10.54 %-100 %. Soil sucrase activity ranged from 0.04 to 0.24 mg·(g·24 h)-1, and those in the U0S10 treatments were significantly higher than those in the U10S0 and CK treatments at all growth stages, increasing by 20.32 % to 99.16 % and 24.31 % to 79.33 %, respectively. ④ The species abundance of bacteria and fungi in maize rhizosphere under all fertilization treatments were lower than those under the CK treatment, followed by those under the U10S0 treatment. The species diversity trend of the bacterial community in the three treatments with ammonium sulfate replacing urea were U8S2 > U0S10 > U6S4, and that of fungi were U6S4 > U8S2 > U0S10. ⑤ The maize dry weight of the U10S0 treatment and U0S10 treatment was the highest, which was 39.47 % and 36.16 % higher than that of the CK treatment, respectively, but the difference was not significant. The Pearson model showed that the species abundance and diversity of soil rhizosphere fungi and bacteria were affected by relevant environmental variables, among which pH value and soil available nitrogen content were the most important factors affecting microbial diversity. In conclusion, when corn planting in calcareous brown soil, replacing urea with a certain proportion of ammonium sulfate can improve soil nutrients more than urea alone, which affects the growth and rhizosphere microbial community of corn to a certain extent and has a greater yield.

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

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

Characterizations of multi-kingdom gut microbiota in immune checkpoint inhibitor-treated hepatocellular carcinoma

BackgroundThe association between gut bacteria and the response to immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) has been studied; however, multi-kingdom gut microbiome alterations and interactions in ICI-treated HCC...

Artificial light at night decreases phyllosphere microbial diversity and functionality in grassland plants

With the rapid expansion of artificial light in the global nocturnal environment, the ecological impacts of artificial light at night (ALAN) on plant communities have garnered increasing research interest. However, the role of phyllosphere microorganisms as mediators in the regulation between ALAN and plants remains unclear. In this study, we conducted a field experiment in natural grassland plots, employing two treatments: one with no artificial light at night (control) and another with artificial light at night (ALAN). We then investigated the response of phyllosphere microorganisms in three grassland plant species (Leymus chinensis, Vicia sepium, and Aster altaicus) to ALAN exposure. The results revealed that the constructive species L. chinensis demonstrated a markedly higher diversity of phyllosphere bacteria and fungi compared to V. sepium and A. altaicus and thus had the most abundant microbial community. However, ALAN exposure reduced the diversity of phyllosphere bacteria and fungi in all three plant species to varying degrees. ALAN induced certain changes to the phyllosphere bacterial community composition, particularly manifesting in a reduction in the abundance of beneficial bacteria, including Sphingomonas, Hymenobacter, Methylobacterium-Methylorubrum, and Bacillus. Compared with phyllosphere bacterial communities, the alterations in phyllosphere fungal communities were more sensitive, characterized by a significant decrease in the abundance of certain fungi, including Zymoseptoria, Mycosphaerella, Cladosporium, and Epicoccum. The functional predictions of phyllosphere bacteria and fungi further corroborate these conclusions. In summary, ALAN exposure may suppress the functional capacity of phyllosphere microorganisms in grassland plants while decreasing the probability of fungal pathogen occurrence.

Bacteria colonization and gene expression related to immune function in colon mucosa is associated with growth in neonatal calves regardless of live yeast supplementation

BackgroundAs Holstein calves are susceptible to gastrointestinal disorders during the first week of life, understanding how intestinal immune function develops in neonatal calves is important to promote better intestinal health. Feeding probiotics in early life may contribute to host intestinal health by facilitating beneficial bacteria colonization and developing intestinal immune function. The objective of this study was to characterize the impact of early life yeast supplementation and growth on colon mucosa-attached bacteria and host immune function.ResultsTwenty Holstein bull calves received no supplementation (CON) or Saccharomyces cerevisiae boulardii (SCB) from birth to 5 d of life. Colon tissue biopsies were taken within 2 h of life (D0) before the first colostrum feeding and 3 h after the morning feeding at d 5 of age (D5) to analyze mucosa-attached bacteria and colon transcriptome. Metagenome sequencing showed that there was no difference in α and β diversity of mucosa-attached bacteria between day and treatment, but bacteria related to diarrhea were more abundant in the colon mucosa on D0 compared to D5. In addition, qPCR indicated that the absolute abundance of Escherichia coli (E. coli) decreased in the colon mucosa on D5 compared to D0; however, that of Bifidobacterium, Lactobacillus, and Faecalibacterium prausnitzii, which could competitively exclude E. coli, increased in the colon mucosa on D5 compared to D0. RNA-sequencing showed that there were no differentially expressed genes between CON and SCB, but suggested that pathways related to viral infection such as “Interferon Signaling” were activated in the colon mucosa of D5 compared to D0.ConclusionsGrowth affected mucosa-attached bacteria and host immune function in the colon mucosa during the first 5 d of life in dairy calves independently of SCB supplementation. During early life, opportunistic pathogens may decrease due to intestinal environmental changes by beneficial bacteria and/or host immune function. Predicted activation of immune function-related pathways may be the result of host immune function development or suggest other antigens in the intestine during early life. Further studies focusing on the other antigens and host immune function in the colon mucosa are required to better understand intestinal immune function development.

Microbiota of Peri-Implant Healthy Tissues, Peri-Implant Mucositis, and Peri-Implantitis: A Comprehensive Review.

Understanding the microbiological profiles of peri-implant conditions is crucial for developing effective preventive and therapeutic strategies. This narrative review analyzes the microbial profiles associated with healthy peri-implant sites, peri-implant mucositis, and peri-implantitis, along with related microbiological sampling and analyses. Healthy peri-implant sites are predominantly colonized by Streptococcus, Rothia, Neisseria, and Corynebacterium species, in addition to Gram-positive cocci and facultatively anaerobic rods, forming a stable community that prevents pathogenic colonization and maintains microbial balance. In contrast, peri-implant mucositis shows increased microbial diversity, including both health-associated and pathogenic bacteria such as red and orange complex bacteria, contributing to early tissue inflammation. Peri-implantitis is characterized by even greater microbial diversity and a complex pathogenic biofilm. Predominant pathogens include Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, and unique species like Filifactor alocis and Fretibacterium fastidiosum. Additionally, less common species such as Staphylococcus and Enterobacteriaceae, contributing to disease progression through biofilm formation and increased inflammatory response, along with EBV and human cytomegalovirus with a still not defined role, and Candida albicans contribute to disease progression through biofilm formation, immune modulation, and synergistic inter-kingdom interactions. Future research should standardize diagnostic criteria, employ advanced molecular techniques, integrate microbial data with clinical factors, and highlight inter-kingdom interactions.

Diversity of marine bacteria growing on leachates from virgin and weathered plastic: Insights into potential degraders.

Plastic debris in the ocean releases chemical compounds that can be toxic to marine fauna. It was recently found that some marine bacteria can degrade such leachates, but information on the diversity of these bacteria is mostly lacking. In this study, we analysed the bacterial diversity growing on leachates from new low-density polyethylene (LDPE) and a mix of naturally weathered plastic, collected from beach sand. We used a combination of Catalysed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH), BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT), and 16S rRNA gene amplicon sequencing to analyse bacterioplankton-groups specific activity responses and the identity of the responsive taxa to plastic leachates produced under irradiated and non-irradiated conditions. We found that some generalist taxa responded to all leachates, most of them belonging to the Alteromonadales, Oceanospirillales, Nitrosococcales, Rhodobacterales, and Sphingomonadales orders. However, there were also non-generalist taxa responding to specific irradiated and non-irradiated leachates. Our results provide information about bacterial taxa that could be potentially used to degrade the chemicals released during plastic degradation into seawater contributing to its bioremediation.