Total Bacterial Community Research Articles

Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile

BackgroundAquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance.ResultsThe taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site.ConclusionsOur results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities’ risk for antibiotic resistance, and that a human—influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.

Impact of organic carbon composition on bacterial taxa assembly upon phosphorus addition in organic and mineral soil layers of a Robinia pseudoaccacia plantation

Increasing phosphorus (P) inputs significantly affect the nutrient cycle of terrestrial ecosystems. The community structure and assembly processes of soil bacteria, which are the primary participants in nutrient cycling within terrestrial ecosystems, are affected by P inputs. However, the assembly processes and driving mechanisms of soil bacterial communities in artificial forest ecosystems in response to P inputs remain unclear. Therefore, in this study, we conducted in situ experimental P additions (0, 0.5, 1, 2, and 4 g P m-2 year-1) to artificial Robinia pseudoacacia forests on the Loess Plateau. We investigated the effects of P addition on the soil organic carbon (SOC) composition, bacterial community characteristics (total, abundant, and rare taxa), and assembly processes in the organic horizon (OH) and mineral horizon (MH) layers of the soil. The results showed that P addition significantly changed soil physicochemical factors, such as available P (AP), SOC content, and SOC composition in terms of the labile (LC) and recalcitrant carbon (RC) fractions. The proportion of the LC fraction increased in OH and decreased in MH, whereas the RC fraction showed the opposite trends. P addition increased the proportion of eutrophic bacteria in OH, whereas it decreased the proportion of oligotrophic bacteria. In contrast to those in OH, the changes in eutrophic and oligotrophic bacteria in MH exhibited the opposite trend. With increasing P levels, the diversity of the bacterial communities in the OH did not change significantly. In the MH, total and rare taxa diversity increased, while the diversity of abundant taxa decreased. During P addition, the total and rare taxa bacterial communities showed stochastic assembly, whereas the assembly of abundant taxa shifted from stochastic to deterministic processes in the OH and from deterministic to stochastic processes in the MH. The structural equation model revealed that during P addition, the assembly of total and rare bacterial communities in the OH and MH was regulated by AP and the LC fraction, respectively. Meanwhile, the assembly of abundant taxa in OH and MH was influenced by the LC fraction and RC fraction, respectively. Our findings highlight the critical role of SOC composition across different bacterial taxa, with abundant bacterial taxa exhibiting heightened sensitivity to environmental filtration and the availability of SOC resources. Our study provides new insights into the community assembly and driving mechanisms of soil bacteria in artificial forest soils during P addition.

Revealing the characteristics of myxobacterial communities in rhizosphere and non-rhizosphere soils of halophytic plants following wetland degradation using high-throughput sequencing

Myxobacteria represent a distinct group in soil microbial communities, with their predatory capabilities playing a vital role in regulating and stabilizing these communities. However, the characteristics of myxobacterial communities in the soils of Karelinia caspia (KC), a halophytic plant growing in degraded wetlands, remain unclear. In this study, we investigated myxobacterial communities in rhizosphere and non-rhizosphere soils from nine KC’ sampling sites in saline-alkaline land formed after wetland degradation using high-throughput sequencing. A total of 486 myxobacterial ASVs were identified from both rhizosphere and non-rhizosphere soil samples, comprising 2.68% of the total bacterial community. The dominant genera at the genus level were Unclassified_g_bacteriap25 and Haliangium. FAPROTAX functional predictions indicated that myxobacteria in rhizosphere soils performed various ecological functions, such as predation, organic matter decomposition, and cellulose degradation, while in non-rhizosphere soils, they primarily displayed predatory functions. The high proportion of unclassified functions suggests that many aspects of myxobacteria in soil remain unexplored. Correlation analysis showed that electrical conductivity, soil moisture, and total nitrogen significantly affected myxobacterial diversity and abundance. Co-occurrence network analysis revealed multiple associations between myxobacteria and other bacterial groups, highlighting their crucial role in maintaining the dynamic equilibrium of soil bacterial communities. These findings deepen our understanding of the relationship between microbial community dynamics and environmental factors, laying a strong foundation for future research in soil microbial ecology and conservation strategies.

Bacterial seed endophytes promote barley growth and inhibits Fusarium graminearum in vitro

ObjectivesSeeds host microbes that function in plant growth and phytopathogen resistance. The aim of the work was to investigate total bacterial community in malting barley seeds and whether their bacterial seed endophytes have dual functional roles in plant growth-promotion and inhibition of Fusarium graminearum, the causative agent of Fusarium head blight (FHB) in barley. We used culture dependent and culture independent methods.ResultsPhylogenetic classification of seed endophytic bacteria based on sequencing data identified B. subtilis, B. licheniformis and B. pumilis as predominant subgroups. Location driven divergence in bacterial endophytic communities was evident based on a clear separation of the samples from Crookston and other location samples. The bio-primed seeds using one hundred and seventy bacterial isolates showed that 3.5% (6/170) of the bacterial isolates conferred greater than 10% increase in both root length (RL) and shoot length (SL), while 19.4% (33/170) and 26.5% (45/170) showed RL and SL specific growth effects, respectively, relative to controls. Among the six bacterial isolates that increased RL and SL, five (#29, #63, #109, #124 and #126) also significantly inhibit the growth of F. graminearum based on in vitro assays. This study identified novel seed bacterial endophytes that could be further exploited for promoting growth during seedling establishment and as biocontrol for combating the devastating scab disease.

Gut Microbiota Diversity of Local Egyptian Cattle Managed in Different Ecosystems.

The animal gastrointestinal tract contains a complex microbiome whose composition ultimately reflects the co-evolution of microorganisms with their animal host and their host's environment. This study aimed to gain insights into the adaptation of the microbiota of local Egyptian cattle to three different ecosystems (Upper Egypt, Middle Egypt, and Lower Egypt) distributed across 11 governorates (with an average of 12 animals per governorate) using amplicon sequencing. We analyzed the microbiota from 136 fecal samples of local Egyptian cattle through a 16S rRNA gene sequencing approach to better understand the fecal microbial diversity of this breed which developed under different ecosystems. An alpha diversity analysis showed that the fecal microbiota of the Egyptian cattle was not significantly diverse across areas, seasons, sexes, or farm types. Meanwhile, microbiota data revealed significant differences in richness among age groups (p = 0.0018). The microbial community differed significantly in the distribution of its relative abundance rather than in richness across different ecosystems. The taxonomic analysis of the reads identified Firmicutes and Actinobacteriota as the dominant phyla, accounting for over 93% of the total bacterial community in Egyptian cattle. Middle Egypt exhibited a different microbial community composition compared to Upper and Lower Egypt, with a significantly higher abundance of Firmicutes and Euryarchaeota and a lower abundance of Actinobacteriota in this region than the other two ecosystems. Additionally, Middle Egypt had a significantly higher relative abundance of the Methanobacteriaceae family and the Methanobrevibacter genera than Lower and Upper Egypt. These results suggest a difference in the adaptation of the fecal microbial communities of Egyptian cattle raised in Middle Egypt. At the genus level, eleven genera were significantly different among the three ecosystems including Bacillus, DNF00809, Kandleria, Lachnospiraceae_NK3A20_group, Methanobrevibacter, Mogibacterium, Olsenella, Paeniclostridium, Romboutsia, Turicibacter, and UCG-005. These significant differences in microbiota composition may impact the animal's adaptation to varied environments.

A Pilot Study for the Characterization of Bacillus spp. and Analysis of Possible B. thuringiensis/Strongyloides stercoralis Correlation.

Differentiating between Bacillus species is relevant in human medicine. Bacillus thuringiensis toxins might be effective against Strongyloides stercoralis, a nematode causing relevant human morbidity. Our first objective was to evaluate genomic and MALDI-TOF identification methods for B. thuringiensis. Our secondary objective was to evaluate a possible negative selection pressure of B. thuringiensis against S. stercoralis. PCR and Sanger were compared to MALDI-TOF on a collection of 44 B. cereus group strains. B. thuringiensis toxin genes were searched on 17 stool samples from S. stercoralis-infected and uninfected dogs. Metagenomic 16S rRNA was used for microbiome composition. The inter-rate agreement between PCR, Sanger, and MALDI-TOF was 0.631 k (p-value = 6.4 × 10-10). B. thuringiensis toxins were not found in dogs' stool. Bacteroidota and Bacillota were the major phyla in the dogs' microbiome (both represented >20% of the total bacterial community). Prevotella was underrepresented in all Strongyloides-positive dogs. However, the general composition of bacterial communities was not significantly linked with S. stercoralis infection. The genomic methods allowed accurate differentiation between B. thuringiensis and B. cereus. There was no association between B. thuringiensis and S. stercoralis infection, but further studies are needed to confirm this finding. We provide the first descriptive results about bacterial fecal composition in dogs with S. stercoralis infection.

Stable-isotope probing combined with amplicon sequencing and metagenomics identifies key bacterial benzene degraders under microaerobic conditions

The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and 13C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of “heavy” and “light” DNA fractions. Results shed light on the fact that the availability of oxygen strongly determined the structure of the degrading bacterial communities. While members of the genus Pseudomonas were overwhelmingly dominant under clear aerobic conditions, they were almost completely replaced by members of genera Malikia and Azovibrio in the microaerobic microcosms. Investigation of the density resolved DNA fractions further confirmed the key role of these two latter genera in the microaerobic degradation of benzene. Moreover, analysis of a previously acquired metagenome-assembled Azovibrio genome suggested that benzene was degraded through the meta-cleavage pathway by this bacterium, with the help of a subfamily I.2.I-type catechol 2,3-dioxygenase. Overall, results of the present study implicate that under limited oxygen availability, some potentially microaerophilic bacteria play crucial role in the aerobic degradation of aromatic hydrocarbons.

Full-length 16S rRNA gene sequencing reveals the operating mode and chlorination-aggravated SWRO biofouling at a nuclear power plant.

Reverse osmosis (RO) membrane fouling and biological contamination problems faced by seawater desalination systems are microbiologically related. We used full-length 16S rRNA gene sequencing to assess the bacterial community structure and chlorine-resistant bacteria (CRB) associated with biofilm growth in different treatment processes under the winter mode of a chlorinated seawater desalination system in China. At the outset of the winter mode, certain CRB, such as Acinetobacter, Pseudomonas, and Bacillus held sway over the bacterial community structure, playing a pivotal role in biofouling. At the mode's end, Deinococcus and Paracoccus predominated, with Pseudomonas and Roseovarius following suit, while certain CRB genera still maintained their dominance. RO and chlorination are pivotal factors in shaping the bacterial community structure and diversity, and increases in total heterotrophic bacterial counts and community diversity in safety filters may adversely affect the effectiveness of subsequent RO systems. Besides, the bacterial diversity and culturable biomass in the water produced by the RO system remain high, and some conditionally pathogenic CRBs pose a certain microbial risk as a source of drinking water. Targeted removal of these CRBs will be an important area of research for advancing control over membrane clogging and ensuring water quality safety in the future.

Impact of two acquisitive plants on N cycle on different soils: The invasive Fallopia japonica does it and so does the native Dactylis glomerata!

Invasive plants may alter ecological and ecosystem processes, including the N-cycle. The Fallopia species complex is a well-studied invasive species whose N-resource acquisition traits define it as an acquisitive species. However, the study of the impacts of invasive plants on the N-cycle never considers the N-acquisition strategy as a reference for choosing another suitable plant control. The purpose of this study is to assess the impacts of an invasive species (Fallopia japonicaFJ) on the N-cycle and to compare with those caused by a native acquisitive species (Dactylis glomerataDG), all compared to unplanted soils. A four-months mesocosm experiment was conducted by growing FJ and DG on nine different soils and measuring their impacts on N-cycle microbial activities (free-living nitrogen fixation FLNF, denitrification DEA, nitrification NEA), on N-mineral forms and on functional N-cycle gene abundance (nifH, AOA, AOB, nirS, nirK) as well as the total bacterial community gene (rRNA 16S). The nine soils differ in microbial enzymatic activities, N-mineral form concentrations, physico-chemical factors, texture, and gene abundances. Plant effects on FLNF, NEA and DEA are only soil dependent and no effect of invasive status was found. In addition, the native plant DG generally affected microbial parameters over a wider range of soils than the invasive plant. Stronger impacts of the native DG on microbial gene abundances were found compared to the invasive FJ. A stronger effect of the invasive plant was found for the soil NO3− concentration, with a significant decrease under the FJ than under the DG. Under both FJ and DG, NH4+ concentrations were not significantly affected. In conclusion, the invasive status in the ecosystem of the two plants studied cannot be explained through their impacts on microbial enzymatic activities and gene abundances of the soil N-cycle and the soil N mineral pools.

Microplastics exert minor influence on bacterial community succession during the aging of earthworm (Lumbricus terrestris) casts

The soil microbiome, which is shaped by gut-related activities of earthworms, is affected by microplastic contamination. However, the influence of microplastics on earthworm gut and cast microbiomes has been poorly explored. Here, we investigated the influence of microplastics (1% in soil, w/w) on soil physicochemical properties and bacterial communities during gut passage and cast aging of Lumbricus terrestris. Microplastics used in agricultural film production were selected, i.e., low density polyethylene, polylactic acid and polybutylene adipate terephthalate (PBAT). Different niches, including pre-ingestion soil, gut content and aged casts (from 0 to 180 days), were studied. Results showed that microplastics possibly enhanced the gut passage-derived difference between pre-ingestion soil and fresh cast in terms of pH, ammonium, nitrate and nitrite, and dissolved organic carbon. But such effects mostly faded out after 180 days of aging. The composition, as well as the alpha and beta diversity of both the total (DNA) and active (RNA) bacterial communities were decisively shaped by their niche (R2: 0.22–0.63, p < 0.001, PERMANOVA), rather than the presence/absence or the types of MPs. Nevertheless, biomarkers indicative of PBAT treatment were identified, and functional prediction for the active community showed that bacterial communities of this treatment had higher potentials for hydrocarbon degradation (4.9–7.8 times that of the microplastic-free treatment in gut and aged casts). We also identified a “Soil-related core community” and a “Gut-related core community” (contributing to 39.2%–50.2% of the cast microbiome), which possibly neutralized microplastic impacts and maintained the structure and function of bacterial communities during the soil–gut–cast transit. Our findings indicate that the tested microplastics exerted a minor influence on the bacterial communities during the cast aging process, microplastics in aged casts might not necessarily have significant additional influence on the soil microbiome when they are incorporated into soils. Future studies testing different soils, polymers, and earthworm species, under field conditions are recommended to help enhance current knowledge of the influence of microplastics on earthworm cast microbiomes.

Bacterial Communities on Degraded Prehistoric Rock Paintings in Maros-Pangkep Global Geopark

391 Bacterial Communities on Degraded Prehistoric Rock Paintings in Maros-Pangkep Global Geopark Nur Haedar1*, Muhammad Iqram1, Ambeng1, Yusriana2, Dody Priosambodo1, and Rustan Lebe3 1Biology Department, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar 90245 Indonesia 2Archaeology Department, Faculty of Cultural Science, Hasanuddin University, Makassar 90245 Indonesia 3Indonesian Heritage Agency, Ministry of Education, Culture, Research, and Technology, Jakarta 10110 Indonesia The Maros-Pangkep karst region is a natural landscape located inside the UNESCO Global Geopark, extending across two regencies in South Sulawesi. There are at least 135 prehistoric caves, of which about 78 of them still have traces of relics in the form of rock paintings. One thing that has made this region renowned is the presence of the world’s oldest ancient rock painting, ca. 40,000 years old, in an ancient cave. Unfortunately, many paintings have been experiencing degradation marked by color changes and exfoliation, which are thought to be partially caused by the colonization of bacterial biofilms. The present study, therefore, aimed to delineate the bacterial diversity of biofilms present in ancient rock paintings. Samples were collected from three different caves in the region and analyzed using Oxford Nanopore Technology, sequencing the full-length 16S rRNA gene (V1–V9 regions). The results showed that Firmicutes was the dominant bacterial taxon in both Leang Jing and Leang Parewe, representing 95 and 82% of the total bacterial community, respectively. In Leang Bulu Sipong, we observed a high relative abundance of both Betaproteobacteria (30%) and Firmicutes (44%). Among the taxa detected, some genera – including Cupriavidus, Bacillus, Lysinibacillus, Paenibacillus, Geobacillus, and Pseudomonas – are linked to the carbonate precipitation and rock weathering, which could give a clue on the role of bacterial activities in corroborating the biodegradation on the ancient rock arts. Despite the result of microbial diversity in the rock paintings, it is necessary to do further study on the mechanism of degradation performed by the bacteria. This will support the effort of local authorities to conserve local heritage aged a thousand years.

Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops.

Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared a similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared with those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All of the examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared with the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence the bacterial and diazotrophic community composition of any of these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced the community composition and function of these biocrusts.

Abundant Species Govern the Altitude Patterns of Bacterial Community in Natural and Disturbed Subalpine Forest Soils

Abundant and rare bacteria exhibit unequal responses to environmental changes and disturbances, potentially resulting in differential contributions to the altitudinal characteristics of total community in natural and disturbed soils. Although the altitude patterns of soil bacteria have been widely studied, it remains unclear whether these patterns are consistent among bacteria with varying predominance levels, and which subpopulation contributes more to maintaining these patterns in natural and disturbed subalpine forest soils. In this study, we collected 18 natural subalpine forest soil samples and 18 disturbed ones from three altitudes (2900 m a.s.l., 3102 m a.s.l., and 3194 m a.s.l.) along the Wenma highway in Miyaluo, Lixian, Sichuan, Southwest China. By partitioning total bacterial communities based on species predominance, we found that bacteria with higher predominance levels tended to exhibit altitude patterns (α-diversity, community structure, and functional redundancy) similar to those of total bacteria in both natural and disturbed subalpine forest soils, although they only occupied a small portion of the community. Abundant bacteria might play critical roles in maintaining the regional ecological characteristics of total community across the altitude gradient, while the rare and hyper-rare ones might contribute more to local diversity and functional redundancy. In natural soils, the altitude patterns of α-diversity inferred from total, abundant, and rare bacteria were mainly shaped by NO3−-N, while soil conductivity mainly drove the altitude patterns of α-diversity inferred from hyper-rare bacteria. Additionally, the community structures of total, abundant, rare, and hyper-rare bacteria were mainly shaped by NO3−-N, while the altitude patterns of functional redundancy inferred from total, abundant, and rare bacteria were mainly shaped by soil conductivity in natural soils. In disturbed subalpine forest soils, the influences of NO3−-N for the altitude patterns of α-diversity and community structure, and those of soil conductivity for functional redundancy, were relatively weak in total, abundant, rare, and hyper-rare bacteria. This study examined the roles of bacteria with varying predominance levels in maintaining the altitude pattern of bacteria in both natural and disturbed subalpine forest soils, providing novel insights for devising strategies to conserve biodiversity and ecologically restore disturbed soils in subalpine ecosystems.

Effects of γ-polyglutamic acid supplementation on alfalfa growth and rhizosphere soil microorganisms in sandy soil

This study aimed at exploring the effects of γ-polyglutamic acid on the growth of desert alfalfa and the soil microorganisms in the rhizosphere. The study examined the effects of varying concentrations of γ-polyglutamic acid (0%-CK, 2%-G1, 4%-G2, 6%-G3) on sandy soil, the research investigated its impact on the growth characteristics of alfalfa, nutrient content in the rhizosphere soil, and the composition of bacterial communities. The results indicated that there were no significant differences in soil organic matter, total nitrogen, total phosphorus, total potassium, and available phosphorus content among the G1, G2, and G3 treatments. Compared to CK, the soil nutrient content in the G2 treatment increased by 14.81–186.67%, showing the highest enhancement. In terms of alfalfa growth, the G2 treatment demonstrated the best performance, significantly increasing plant height, chlorophyll content, above-ground biomass, and underground biomass by 54.91–154.84%. Compared to the CK treatment, the number of OTUs (operational taxonomic units) in the G1, G2, and G3 treatments increased by 14.54%, 8.27%, and 6.84%, respectively. The application of γ-polyglutamic acid altered the composition and structure of the bacterial community, with Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota accounting for 84.14–87.89% of the total bacterial community. The G2 treatment significantly enhanced the diversity and evenness of soil bacteria in the rhizosphere. Redundancy analysis revealed that organic matter, total nitrogen, total potassium, moisture content, and pH were the primary factors influencing the structure of bacterial phyla. At the genus level, moisture content emerged as the most influential factor on the bacterial community. Notably, moisture content exhibited a strong positive correlation with Acidobacteriota, which in turn was positively associated with indicators of alfalfa growth. In summary, the application of γ-polyglutamic acid at a 4% ratio has the potential for improving sandy soil quality, promoting plant growth, and regulating the rhizosphere microbial community.

Deciphering bacterial community structure in Cola lepidota (K.) Schum fruits using Illumina next-generation sequencing

Cola lepidota cultivation is hampered by pathogenic microorganisms which affect the quality and quantity of produce after harvest. Bacterial organisms cause softening of tissues which may lead to the spoilage of the whole fruit. This study aimed to detect the bacterial organisms and the bacterial community structure associated with monkey cola (Cola lepidota K. Schum) fruits using Illumina next-generation sequencing (NGS). Amplification of the v4 regions of the 16S rDNA gene was performed through Polymerase chain reaction (PCR) using the primers, 515F and 806R. Picking of the Operational Taxonomic Units (OTUs) and assignment of the OTUs into different taxonomic levels were performed on GREENGENES database. The most abundant phyla obtained from Cola lepidota mesocarp and seeds were Proteobacteria (40.83 %), Bacteroidetes (31.01 %) and Firmicutes (24.52 %). The abundance of Bacteroides, which was the predominant genus in the majority of the samples, was between 31 and 72 % among the total bacteria identified in most samples. Other relatively high abundant genera obtained across the total bacterial community of C. lepidota were Pseudomonas (19.20 %), Tepidimonas (13.76 %) and Acinetobacter (13.33 %). We obtained potentially beneficial, human and phytopathogenic microorganisms which play important roles in evolutionary and ecological processes. Among these genera include Acinetobacter and Staphylococcus which are opportunistic human pathogens. This study revealed the bacterial organisms associated with monkey cola fruits and indicates that Illumina next generation sequencing can be used to determine the bacterial community structure and bacterial organisms in fruits.

Habitat-specific patterns of bacterial communities in a glacier-fed lake on the Tibetan Plateau.

Different types of inlet water are expected to affect microbial communities of lake ecosystems due to changing environmental conditions and the dispersal of species. However, knowledge of the effects of changes in environmental conditions and export of microbial assemblages on lake ecosystems is limited, especially for glacier-fed lakes. Here, we collected water samples from the surface water of a glacier-fed lake and its two fed streams on the Tibetan Plateau to investigate the importance of glacial and non-glacial streams as sources of diversity for lake bacterial communities. Results showed that the glacial stream was an important source of microorganisms in the studied lake, contributing 45.53% to the total bacterial community in the lake water, while only 19.14% of bacterial community in the lake water was seeded by the non-glacial stream. Bacterial communities were significantly different between the glacier-fed lake and its two fed streams. pH, conductivity, total dissolved solids, water temperature and total nitrogen had a significant effect on bacterial spatial turnover, and together explained 36.2% of the variation of bacterial distribution among habitats. Moreover, bacterial co-occurrence associations tended to be stronger in the lake water than in stream habitats. Collectively, this study may provide an important reference for assessing the contributions of different inlet water sources to glacier-fed lakes.

The Investigation of Changes in Bacterial Community of Pasteurized Milk during Cold Storage

The quality of pasteurized milk is commonly assessed through microbiological analysis, with variations in storage conditions significantly impacting the suppression of bacterial growth throughout the milk’s shelf life. This study investigated the dynamics of total bacterial counts (TBCs) and bacterial community shifts in milk that underwent pasteurization at 80 °C for 15 s. The milk was subsequently stored at 4 °C for varying intervals of 1, 4, 7, 10, 13, and 16 days. Culture-based testing revealed a significant TBC increase during the storage period spanning 1 to 16 days (up to −log10 4.2 CFU/mL at day 16). The TBC in pasteurized milk exhibited accelerated microbial growth from day 13 onwards, ultimately peaking on day 16. Bacillus was detected through 16S rRNA identification. Principal component analysis demonstrated a significant impact of storage time on bacterial communities in pasteurized milk. Analysis of bacterial diversity revealed a negative correlation between the Shannon index and the duration of pasteurized milk storage. Using high-throughput sequencing, Streptococcus and Acinetobacter were detected as prevalent bacterial genera, with Streptococcus dysgalactiae and Streptococcus uberis showing as dominant taxa. The presence of Streptococcus dysgalactiae and Streptococcus uberis in pasteurized milk might be attributed to the initial contamination from raw milk with mastitis. This study offers new evidence of the prevalence of bacterial community in pasteurized milk, thereby adding value to the enhancement of quality control and the development of strategies for reducing microbial risks.

Investigating microbial and environmental drivers of nitrification in alkaline forest soil.

Ammonia oxidation is a key step in the biogeochemical cycling of nitrogen, and soils are important ecosystems for nitrogen flux globally. Approximately 25% of the world's soils are alkaline. While nitrification has been studied more extensively in agricultural alkaline soils, less is known about natural, unfertilized alkaline soils. In this study, microorganisms responsible for ammonia oxidation and several environmental factors (season, temperature, ammonia concentration, and moisture content) known to affect nitrification were studied in an alkaline forest soil with a pH ranging from 8.36 to 8.77. Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea, and comammox were present, and AOB belonging to genera Nitrosospira and Nitrosomonas, originally comprising <0.01% of the total bacterial community, responded rapidly to ammonia addition to the soil. No significant difference was observed in nitrification rates between seasons, but there was a significant difference between in situ field nitrification rates and rates in laboratory microcosms. Surprisingly, nitrification took place under many of the tested conditions, but there was no detectable increase in the abundance of any recognizable group of ammonia oxidizers. This study raises questions about the role of low-abundance microorganisms in microbial processes and of situations where zero or very low microbial growth coincides with metabolic activity. In addition, this study provides insights into nitrification in unfertilized alkaline soil and supports previous studies, which found that AOB play an important role in alkaline soils supplemented with ammonia, including agricultural ecosystems.

Coupling between 2, 2′, 4, 4′-tetrabromodiphenyl ether (BDE-47) debromination and methanogenesis in anaerobic soil microcosms

Polybrominated diphenyl ethers (PBDEs) are persistent pollutants that may undergo microbial-mediated debromination in anoxic environments, where diverse anaerobic microbes such as methanogenic archaea co-exist. However, current understanding of the relations between PBDE pollution and methanogenic process is far from complete. To address this knowledge gap, a series of anaerobic soil microcosms were established. BDE-47 (2, 2′, 4, 4′-tetrabromodiphenyl ether) was selected as a model pollutant, and electron donors were supplied to stimulate the activity of anaerobes. Debromination and methane production were monitored during the 12 weeks incubation, while obligate organohalide-respiring bacteria (OHRBs), methanogenic, and the total bacterial communities were examined at week 7 and 12. The results demonstrated slow debromination of BDE-47 in all microcosms, with considerable growth of Dehalococcoides and Dehalogenimonas over the incubation observed in most BDE-47 spiked treatments. In addition, the accumulation of intermediate metabolites positively correlated with the abundance of Dehalogenimonas at week 7, suggesting potential role of these OHRBs in debromination. Methanosarcinaceae were identified as the primary methanogenic archaea, and their abundance were correlated with the production of debrominated metabolites at week 7. Furthermore, it was observed for the first time that BDE-47 considerably enhanced methane production and increased the abundance of mcrA genes, highlighting the potential effects of PBDE pollution on climate change. This might be related to the inhibition of reductive N- and S-transforming microbes, as revealed by the quantitative microbial element cycling (QMEC) analysis. Overall, our findings shed light on the intricate interactions between PBDE and methanogenic processes, and contribute to a better understanding of the environmental fate and ecological implication of PBDE under anaerobic settings.

Large-Scale Biogeographical Shifts of Abundance of Antibiotic Resistance Genes and Marine Bacterial Communities as Their Carriers along a Trophic Gradient.

The role of marine environments in the global spread of antibiotic resistance still remains poorly understood, leaving gaps in the One Health-based research framework. Antibiotic resistance genes (ARGs) encoding resistance to five major antibiotic classes, including sulfonamides (sul1, sul2), tetracyclines (tetA, tetB), β-lactams (blaCTX-M, blaTEMblaVIM), macrolides (ermB, mphA), aminoglycosides (aac3-2), and integrase gene (intl1) were quantified by RT-qPCR, and their distribution was investigated in relation to environmental parameters and the total bacterial community in bottom layer and surface waters of the central Adriatic (Mediterranean), over a 68 km line from the wastewater-impacted estuary to coastal and pristine open sea. Seasonal changes (higher in winter) were observed for antibiotic resistance frequency and the relative abundances of ARGs, which were generally higher in eutrophic coastal areas. In particular, intl1, followed by blaTEM and blaVIM, were strongly associated with anthropogenic influence and Gammaproteobacteria as their predominant carriers. Water column stratification and geographic location had a significant influence on ARGs distribution in the oligotrophic zone, where the bacterial community exhibited a seasonal shift from Gammaproteobacteria in winter to Marine group II in summer.