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The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined. [ABSTRACT FROM AUTHOR]

We identified full-length sequence of a potexvirus infecting Nerine plants in the UK. By sequencing viruses in historical collections we have been able to demonstrate that the identified virus, for which we propose the name nerine potexvirus 1, is a potentially novel species in the genus Potexvirus. Analysis of the potexviruses in the historic collections has also enabled us to generate the first full-length sequence of nerine virus X (NVX) to be isolated from Nerine; and to clarify the taxonomy of NVX isolates infecting Nerine and Agapanthus. Analysis of isolates from the historical collections has enabled us to link biological data gathered in the pre-genomic era to specific isolate sequences. [ABSTRACT FROM AUTHOR]

The diversity, composition, and abundance of soil fungi from three sacred groves in Kerala, namely Iringole kavu of Ernakulam District, Kollakal Thapovanam of Alappuzha District, and Poyilkavu of Kozhikode District were analysed using Metagenomics analysis and Illumina sequencing. A total of 30,584, 78,323, and 55,640 reads were obtained from these groves, respectively. Ascomycota constitutes over 96% of the total fungi, making it the most abundant phylum, followed by Mortierellomycota, Basidiomycota, Chytridiomycota, and Rozellomycota. These phyla were subdivided into 20 classes, 40 orders, 83 families, 119 genera, and 135 species, while 1269 OTUs remained unidentified at the species level. Eurotiomycetes predominates the class, while the genus Talaromyces from the family Trichomaceae dominates the genera. Neocarmospora falciformis, Trichoderma lixii, and Candida ethanolic are the most abundant fungal species. Diversity analysis shows that Kollakal Thapovanam is rich in fungal species, while Poyilkavu is rich in biodiversity, with a high degree of dominance. Several species were found only in a particular grove and were absent in others and vice-versa, indicating high fungal specificity. Therefore, fungi have to be preserved in their original habitat. The Principal Coordinate Analysis revealed that each grove is distinct highlighting the importance of preserving the unique diversity of each sacred grove. In conclusion, this research provides valuable information about the soil fungal genera in their natural habitat. It emphasizes the need for more systematic research to understand the actual diversity and ecological role of fungi in sacred groves. This study is the first of its kind to analyse and compare soil fungal diversity in sacred groves using the metagenomics approach. [ABSTRACT FROM AUTHOR]

Background: The genus Ternstroemia is associated with the vulnerable tropical montane cloud forest in Mexico and with other relevant vegetation types worldwide. It contains threatened and pharmacologically important species and has taxonomic issues regarding its species limits. This study describes 38 microsatellite markers generated using a genomic-based approach. Methods and results: We tested 23 of these markers in a natural population of Ternstroemia lineata. These markers are highly polymorphic (all loci polymorphic with 3–14 alleles per locus and expected heterozygosity between 0.202 and 0.908), most of them (19 out of 23) are in Hardy-Weinberg Equilibrium and free of null alleles (18 out of 23). Also we found no evidence of linkage among them. Finally, we tested the transferability to six other American species of Ternstroemia, two other Pentaphylacaceae species, and four species from different families within the order Ericales. Conclusions: These molecular resources are promising tools to investigate genetic diversity loss and as barcodes for ethnopharmacological applications and species delimitation in the family Pentaphylacaceae and some Ericales, among other applications. [ABSTRACT FROM AUTHOR]

Isolation of heavy metals-resistant bacteria from their original habitat is a crucial step in bioremediation. Six lead (Pb) resistant bacterial strains were isolated and identified utilizing 16S rRNA to be Enterobacter ludwigii FACU 4, Shigella flexneri FACU, Microbacterium paraoxydans FACU, Klebsiella pneumoniae subsp. pneumonia FACU, Raoultella planticola FACU 3 and Staphylococcus xylosus FACU. It was determined that all these strains had their Minimum inhibitory concentration (MIC) to be 2500 ppm except R. planticola FACU 3 has a higher maximum tolerance concentration (MTC) up to 2700 ppm. We evaluated the survival of all six strains on lead stress, the efficiency of biosorption and lead uptake. It was found that R. planticola FACU 3 is the highest MTC and S. xylosus FACU was the lowest MTC in this evaluation. Therefore, transmission electron microscopy (TEM) confirmed the difference between the morphological responses of these two strains to lead stress. These findings led to explore more about the genome of R. planticola FACU 3 using illumine Miseq technology. Draft genome sequence analysis revealed the genome size of 5,648,460 bp and G + C content 55.8% and identified 5526 CDS, 75 tRNA and 4 rRNA. Sequencing technology facilitated the identification of about 47 genes related to resistance to many heavy metals including lead, arsenic, zinc, mercury, nickel, silver and chromium of R. planticola FACU 3 strain. Moreover, genome sequencing identified plant growth-promoting genes (PGPGs) including indole acetic acid (IAA) production, phosphate solubilization, phenazine production, trehalose metabolism and 4-hydroxybenzoate production genes and a lot of antibiotic-resistant genes. [ABSTRACT FROM AUTHOR]

Bacteria have a fundamental role in determining the fitness of grapevine, the composition of grapes and the features of wines but at present, little information is available. In this work, the bacteria colonizing the different portions of grapevine (bark, leaves and grapes) were explored in the vineyards of the Alpine region of Trentino, considering the impact of different environmental and agronomical variables. The vineyards included in the work were selected based on their different geographical positions (altitude) and grapevine training systems in order to explore the whole variability of the grapevine ecosystem. Moreover, the surface amount of copper was measured on grapes and leaves during the vegetative growth. Bacterial analysis, performed using plate counts and Illumina MiSeq, revealed an increase in the concentration of grape bacteria proportional to the progress of the ripening stage. Conversely, the peak of bacterial concentration onto leaf and bark samples occurred in August, probably due to the more favourable environmental conditions. In bark samples, the bacterial microbiota reached the 7 log CFU/cm2, while 6 log UFC/g were measured in grape samples. A remarkable biodiversity was observed, with 13 phyla, 35 classes, 55 orders, 78 families and 95 genera of bacteria present. The presence of some taxa (Alphaproteobacteria, Desulfovibrionaceae, Clostriadiales, Oscillospira, Lachnospiraceae and Bacteroidales) was ubiquitous in all vineyards, but differences in terms of relative abundance were observed according to the vegetative stage, altitude of the vineyard and training system. Bacteria having oenological implication (Lactobacillus, Pediococcus and Oenococcus) were detected in grape samples collected in August, in low abundance. The data revealed a complex bacterial ecosystem inside the vineyard that, while maintaining common traits, evolves according to environmental and agronomical inputs. This study contributes to define the role of bacteria in the complex balance established in each vineyard between human actions and agricultural environment, known as terroir. [ABSTRACT FROM AUTHOR]

Background: Biofumigation is a non-chemical sustainable approach that reshapes soil microbiota to overcome challenges in way of continuous cultivation. However, the type and quantity of substrate have a significant impact on microbiota shifts and the subsequent success of biofumigation. Moreover, studies on the effects of biofumigant concentration in combination with fumigation duration on soil microbiota dynamics are very rare. Research methods: We performed microcosm experiments to investigate how a biofumigant (Korean canola cultivar, HanRa) at various concentrations (0.5%, 1%, 2–4% w/w: biofumigant/soil) and fumigation periods (2–4 weeks) affects the soil bacterial and fungal communities. Subsequently, pot experiments employing two Korean canola cultivars (HanRa and YongSan) at 1% (w/w) were carried out. Results: Illumina MiSeq analysis revealed that 2–4% biofumigant, regardless of incubation period, had a significant negative impact on microbial diversity and network complexity. In contrast, 1% biofumigant transformed the bacterial, fungal, and inter-kingdom networks into a highly connected and complex network without affecting microbial diversity. Bacillus, Clostridium, and Pseudomonas were the most highly stimulated bacterial genera in the biofumigated soils, whereas the abundance of Acidobacteria members was greatly reduced. The 2–4% amendments had substantially and more differentially abundant Fusarium than the 1%. Soil nutrition (e.g., pH, nitrate, ammonium, and exchangeable potassium), fruit yield, and weed suppression were enhanced in subsequent pot experiments. Of the nine soil chemical properties, phosphate and exchangeable potassium were the main factors influencing the microbial community assembly. Conclusions: Optimized biofumigation-mediated increase in nitrate, ammonium, and potassium availability in the soil without causing any negative effects on soil microbial diversity indicates its potential as a preplant to improve crop productivity. This study contributes significantly to our understanding of how an optimal biofumigant can help ameliorate obstacles in continuous cropping. [ABSTRACT FROM AUTHOR]

Ulleungdo is a volcanic island with an oceanic climate seasonally affected by warm and cold currents. The freshwater ecosystems of Ulleungdo Island act as an ecological indicator that reveals changes caused by various environmental factors. This study applied Illumina MiSeq to analyze microalgal groups within the eukaryotic microbial community and determine regional differences in microalgal groups inhabiting Ulleungdo Island. Also, we compared the Illumina MiSeq analysis with the culture-based analysis results. The 18S rRNA regions were amplified using an 18S V4 primer set to analyze eukaryotic microbial and microalgal communities. As a result, Basidiomycota (fungi) was the predominant eukaryotic microbial group. The proportion of Chlorophyta (green algae) in the microalgal group was higher than that of Bacillariophyta (diatoms). The microalgal species detected included two diatoms (Achnanthidium minutissimum and Nitzschia palea) and three green algae (Dictyosphaerium spp., Tetradesmus obliquus, and Desmodesmus spp.). Additionally, the composition and species diversity of eukaryotic microbial communities changed according to the environmental factors of each stream or groundwater source. Illumina MiSeq analysis is a powerful tool for overcoming the limitations of culture-based analyses. Therefore, our research provided an enhanced ecological understanding of environmental factors associated with microalgal groups within the eukaryotic microbial community of Ulleungdo Island. [ABSTRACT FROM AUTHOR]

In this study, the microbial community (Bacteria, Archaea, and Fungi) of a historical manuscript was investigated by microscopic observation (field emission scanning electron microscopy), culture-dependent methods, and sequencing of amplicons on the Illumina MiSeq platform. Microbial isolates were also assayed for production of hydrolytic enzymes (cellulase, amylase, and protease). Observation of gold-coated paper samples in high-vacuum mode revealed bacterial cells, conidia, and fungal mycelium among the fibers. Eleven bacterial strains, including species of Bacillus, Streptomyces,Corynebacterium, and four fungal strains, including species of Aspergillus and Alternaria, were isolated by culture-dependent methods and identified by 16S rRNA and ITS sequencing, by comparison with the EzBioCloud and MycoBank databases, respectively. Illumina MiSeq sequencing revealed the presence of 20 bacterial genera, including Pseudomonas,Bacillus, Citrococcus, Promicromonospora, Carnobacterium, Arthrobacter, Salinibacterium, and Streptomyces. According to the number of reads, Pseudomonas (58%) was the most abundant genus and P. stutzeri (55.2%) was the most abundant bacterial species. Sequencing results of fungal amplicons indicated 62 genera, including Penicillium, Aspergillus, Alternaria, Mucor, and Chaetomium. Penicillium (58.89%) and Aspergillus (33.02%) were the most abundant genera. P. polonicum (55.45%) and A. ruber (22.55%) were the most abundant species of the fungal community. The results of searching for archaea in the microbial community of the manuscript by culture-dependent and high-throughput amplicon sequencing were negative. The enzymatic activity of microbial isolates indicated a potential risk of biodeterioration. It seems that using a combination of culture-dependent and high-throughput sequencing methods has a significant advantage over using them individually. [ABSTRACT FROM AUTHOR]

Several studies have investigated palm trees' microbiota infected with red palm weevil (RPW) (Rhynchophorus ferrugineus), the major pest of palm trees. This study compared the microbial communities of infected and uninfected palm trees in the Hail region, Northern Saudi Arabia, determined by high-throughput 16S rRNA gene sequencing by Illumina MiSeq. The results indicated that taxonomic diversity variation was higher for infected tree trunk than the healthy tree trunk. Soil samples from the vicinity of healthy and infected trees did not have a significant variation in bacterial diversity. Myxococcota, Acidobacteriota, and Firmicutes were the dominant phyla in RPW-infected tree trunk, and Pseudomonadaceae was the most prominent family. This study is the first report on the characterization of RPW-infected and healthy palm trees' microbiome. [ABSTRACT FROM AUTHOR]

Oxycarenus laetus is a cotton pest that primarily feeds on seeds that are rich in gossypol. Though gossypol is toxic to general herbivores, O. laetus does not show such complications and instead grows and reproduces well on cotton plants compared to its other hosts. In this study, we have fed O. laetus with natural and induced gossypol-based diets to explore the difference in its gut microbiota. We performed NGS 16S rRNA amplicon sequencing on the Illumina MiSeq platform and analyzed the data using the QIIME2 pipeline supplemented with Greengenes and EZBioCloud reference databases. We also used culture-based methods to identify a few abundant gut bacteria present in O. laetus. Enterococcus faecalis, Wolbachia bourtzisii, Wolbachia pipientis, Corynebacterium glyciniphilum, Staphylococcus sciuri, and Kocuria rosea were some of the major species that formed the core gut microbiome of O. laetus. We have also observed that some species were present only in the sample with the highest concentration of gossypol, signifying that they might have the potential to degrade gossypol. [ABSTRACT FROM AUTHOR]

The hidden diversity and interactions of gall midges (Cecidomyiidae), their associated microfungal symbiont(s), and parasitoid wasps in temperate saltmarshes have been little studied in Australia. Over a period of two years, we investigated the gall-associated communities of the dominant saltmarsh plants, Tecticornia arbuscula and Salicornia quinqueflora, across south-eastern Australian coastal and inland salt-lake sites. We discovered that i) many gall midge species are more widely distributed than previously thought; ii) co-distribution of species affecting different plant organs on the same host is also widespread; iii) diversity of gall midges (6 species previously named; 5 species identified here as new) and parasitoid wasps (17 sp. prov.) is likely higher than we uncovered; iv) parasitoid wasps associated with gall midges belonged to diverse lineages and appear to be widespread generalists; v) while the microfungus usually associated with most Cecidomyiinae larval chambers is Botryosphaeria dothidea, we discovered a provisional new species of Botryosphaeria associated with a novel Asphondylia sp. in western South Australia. We also show that targeted amplicon sequencing is a valuable tool for investigating all components of multi-trophic level systems. Our research has contributed to a greater understanding of the basic biology of gall midge interactions within temperate saltmarsh ecosystems in southern Australia, and highlights the value of investigating all trophic levels in these complex interactions simultaneously. [ABSTRACT FROM AUTHOR]

Probiotics are considered valuable to human health since they improve intestinal microbial balance. Probiotics are orally taken and affect the oral microbiota, which is one of the most important parts of the human microbial community. However, there is little information on the effects of probiotics on the oral microbiota. Caries-free preschool children (N = 6) with complete deciduous dentition were enrolled and given 100 g probiotic yogurt daily for 1 year. Salivary samples were collected every 6 months and then sequenced by Illumina MiSeq system based on 16S rDNA V3–V4 hypervariable regions. The data were analyzed to obtain the changes in microbiota profiles before and after the probiotic yogurt consumption. The α diversity analysis showed that salivary microbial diversity and richness were similar between the groups. The β diversity analysis showed that salivary microbial community structure changed with the consumption of probiotic yogurt. The variation of the microbial community composition was mainly due to 9 genera; for 7 genera (Campylobacter, Haemophilus, Lautropia, Bacillus, Catonella, Lactococcus, and Solibacillus) increased, while 2 genera (Gemella, and Streptococcus) decreased. The variation of salivary microbiota structure and composition with the consumption of probiotic yogurt was revealed. This expands overall insights on the effects of probiotic products on oral microecology. It further provides a basis for predicting possible relations between probiotic interventions and oral health in preschool children. [ABSTRACT FROM AUTHOR]

The spatial structure of the environment is known to affect ecological processes. Unlike the spatial structure of negative interactions, such as competition and predation, the role of spatial structure in positive interaction has received less attention. We tested how the spatial structure of spores of ectomycorrhizal fungi (EMF) in the soil affects the growth of Aleppo pine (Pinus halepensis) seedlings. Spores were spatially distributed at four different levels of patchiness (1 patch, 4 patches, 8 patches and complete mixing) in 4 L pots (all pots received the same total amount of spores). Based on previous findings, we hypothesized that plant performance would gradually increase from the single patch treatment to the complete mixing. However, we found a non-linear response to patchiness. Specifically, plants were largest in the single patch and complete mixing while those in the 4 and 8 patch treatments were the smallest. This non-monotonic response, which might be the result of spatially determined colonization timing or community composition, suggests that the spatial structure of EMF spores has a complex effect on seedling growth. [ABSTRACT FROM AUTHOR]

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Fire effects on ecosystems range from destruction of aboveground vegetation to direct and indirect effects on belowground microorganisms. Although variation in such effects is expected to be related to fire severity, another potentially important and poorly understood factor is the effect of fire seasonality on soil microorganisms. We carried out a large-scale field experiment examining the effects of spring (early-dry season) versus autumn (late-dry- season) burns on the community composition of soil fungi in a typical Mediterranean woodland. Although the intensity and severity of our prescribed burns were largely consistent between the two burning seasons, we detected differential fire season effects on the composition of the soil fungal community, driven by changes in the saprotrophic fungal guild. The community composition of ectomycorrhizal fungi, assayed both in pine seedling bioassays and from soil sequencing, appeared to be resilient to the variation inflicted by seasonal fires. Since changes in the soil saprotrophic fungal community can directly influence carbon emission and decomposition rates, we suggest that regardless of their intensity and severity, seasonal fires may cause changes in ecosystem functioning. [ABSTRACT FROM AUTHOR]

A small percentage of the total freshwater on Earth is represented by river water. Microbes have an essential role to play in the biogeochemical cycles, mineralization of organic water, along with xenobiotics degradation. Microbial dynamics are susceptible to environmental stressors which includes pollutants such as antibiotics, metals, and other degradants. River Yamuna is polluted extensively by domestic and industrial wastes. Xenobiotics, when released into the environment, can lead to water pollution. The present study evaluates the microbial diversity in Yamuna River (28°40′5.53′′ N, 77°15′0.35′′ E) along with the prediction of the metagenome function. In this context, the metagenomic DNA was extracted and sequencing was done on Illumina@MiSeq platform. The total number of OTUs picked was 41,994, out of which 74% were classified within the kingdom Bacteria. 35% of the OTUs were assigned to phylum Proteobacteria, followed by Bacteriodetes (22%), whereas 26% of OTUs were unassigned. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to predict metagenomic functions using 16S rDNA as a marker. Metagenomic reads were assigned to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous (COG), and Gene Ontology (GO). Functional characterization reveals the presence of methyl-accepting chemotaxis protein which is an important adaptation for the microbes in the environment. The enzymes can be mapped for the bioremediation of xenobiotics. Information obtained from the amplicon sequencing of River Yamuna, collaborated with "omic" studies, may help in the design of bioremediation strategies and can be used for environmental clean-up of pollutants. [ABSTRACT FROM AUTHOR]

The diversity and community structure of arbuscular mycorrhizal fungi (AMF) associated with coconut (Cocos nucifera) roots was evaluated by next generation sequencing (NGS) using partial sequences of the 18S rDNA gene and by spore isolation and morphological identification from rhizosphere soil. Root samples from six different Green Dwarf coconut plantations and from one organic plantation surrounded by tropical dry forest along the coastal sand dunes in Yucatan, Mexico, were collected during the rainy and dry seasons. In total, 14 root samples were sequenced with the Illumina MiSeq platform. Additionally, soil samples from the dry season were collected to identify AMF glomerospores. Based on a 95–97% similarity, a total of 36 virtual taxa (VT) belonging to nine genera were identified including one new genus-like clade. Glomus was the most abundant genus, both in number of VT and sequences. The comparison of dry and rainy season samples revealed differences in the richness and composition of AMF communities colonizing coconut roots. Our study shows that the main AMF genera associated with coconut tree roots in all samples were Glomus, Sclerocystis, Rhizophagus, Redeckera, and Diversispora. Based on glomerospore morphology, 22 morphospecies were recorded among which 14 were identified to species. Sclerocystis sinuosa, Sclerocystis rubiformis, Glomus microaggregatum, and Acaulospora scrobiculata were dominant in field rhizosphere samples. This is the first assessment of the composition of AMF communities colonizing coconut roots in rainy and dry seasons. It is of importance for selection of AMF species to investigate for their potential application in sustainable agriculture of coconut. [ABSTRACT FROM AUTHOR]

We aimed to study how seasonal heat stress (i.e., spring vs. summer) influenced microbiota diversity in the dairy cows' feces using Illumina MiSeq sequencing. Sixteen dairy cows were experiencing spring thermoneutral conditions (daily mean temperature = 18.8 ± 3.40 °; daily mean THI = 64.29 ± 4.94) and 16 under summer heat stress (daily mean temperature = 27.63 ± 5.34 °; daily mean THI = 82.56 ± 1.74). Fecal samples were collected per cow three times daily from day 18 to day 22 during each experimental period. Results revealed that the microbiota diversity in the feces was significantly lower (P < 0.05) under summer heat stress. At both the phylum and genera levels, significant differences were observed on microbiota composition in cow's feces between spring and summer. The most dominant phylum was Firmicutes, contributing 69.45% and 87.14% of the fecal microbiota in spring and summer, respectively, followed by Bacteroidetes, contributing 25.27% and 4.45%, respectively. Compared with the dairy cows in the spring season, the relative abundance of unclassified Peptostreptococcaceae, Turicibacter, and Clostridium_sensu_stricto_1 (P < 0.05) were greatly increased (P < 0.05), while the significant decrease in the proportion of Ruminococcaceae_UCG-005 and Rikenellaceae_RC9_gut_group as well as Bacteroides were observed in hot summer. Prediction of microbiota gene function in feces based on PICRUSt method found that different microbiota between spring and summer were mainly concentrated on the function related to membrane transport, infectious diseases, immune system diseases, and lipid metabolism. This study demonstrates that diversity and composition of fecal microbiota in dairy cows varies under different THI condition, and the relationship between fecal microbiota and cows' health needs further research. [ABSTRACT FROM AUTHOR]

Accurate and timely data regarding freshwater fish communities is important for informed decision-making by local, state, tribal, and federal land and resource managers; however, conducting traditional gear-based fish surveys can be an expensive and time-consuming process, particularly in remote areas, like those that characterize much of Alaska. To help address this challenge, we developed and tested five multi-species environmental DNA (eDNA) primer sets for the simultaneous detection of up to 37 target fish species in a single sample. Using these primer sets can reduce the cost and time needed to perform future studies of fish communities. Our results comparing multiple samples from multiple lakes and streams using multiple next-generation sequencing runs show the efficacy and reproducibility of these primers. [ABSTRACT FROM AUTHOR]

Sorgoleone is a secondary sorghum metabolite released from roots. It has allelopathic properties and is considered to inhibit ammonia-oxidizing archaea (AOA) and bacteria (AOB) responsible for the rate-limiting step (ammonia oxidation) in nitrification. Low activity of these microorganisms in soil may contribute to slow down nitrification and reduce nitrogen loss via denitrification and NO3− leaching. The potential nitrification rate (PNR) and the composition of microbial communities were monitored in rhizosphere soil to investigate the growth effect sorghum on biological nitrification inhibition (BNI). A greenhouse pipe experiment was conducted using sorghum lines IS20205 (high-sorgoleone release ability), IS32234 (medium-sorgoleone release ability), 296B (low-sorgoleone release ability), and a control (no plants) combined with fertilization application of 0 or 120 kg N ha−1. We applied nitrogen as ammonium sulfate at 16 days (20 N), 37 days (40 N), and 54 days (60 N). We collected soil solutions at 7.5 cm depths every 3 days and measured the pH and nitrate levels. At 1 and 2.3 months, we sampled the bulk and rhizosphere soils and roots in the 0–10 cm, 10–30 cm, and 30–80 cm depths to determine NO2, mineral N, total N, total C, sorgoleone, the composition of AOA, AOB, and total bacteria and archaea. Sorgoleone was continuously released throughout the 2.3 months' growth and was significantly higher in IS20205, followed by IS32234 then 296B, which showed shallow levels. The IS2020 5rhizosphere showed lower NO2 and nitrate levels and significant inhibition of AOA populations. However, we did not find significant differences in the abundance of AOB between plant treatments. Multivariate analysis and Spearman's correlations revealed that sorgoleone as well as environmental factors such as soil pH, soil moisture, NO3−-N, and NH4+-N shape the composition of microbial communities. This study demonstrated that the release of higher amounts of sorgoleone has great potential to inhibit the abundance of AOA and soil nitrification. The breeding of sorghum lines with the ability to release higher amounts of sorgoleone could be a strategic way to improve the biological nitrification inhibition during cultivation. [ABSTRACT FROM AUTHOR]

Sufficient evidence indicates that orbiting space stations contain diverse microbial populations, which may threaten astronaut health and equipment reliability. Understanding the composition of microbial communities in space stations will facilitate further development of targeted biological safety prevention and maintenance practices. Therefore, this study systematically investigated the microbial community of China's Space Station (CSS). Air and surface samples from 46 sites on the CSS and Assembly Integration and Test (AIT) center were collected, from which 40 bacteria strains were isolated and identified. Most isolates were cold- and desiccation-resistant and adapted to oligotrophic conditions. Bacillus was the dominant bacterial genus detected by both cultivation-based and Illumina MiSeq amplicon sequencing methods. Microbial contamination on the CSS was correlated with encapsulation staff activities. Analysis by spread plate and qPCR revealed that the CSS surface contained 2.24 × 103–5.47 × 103 CFU/100 cm2 culturable bacteria and 9.32 × 105–5.64 × 106 16S rRNA gene copies/100cm2; BacLight™ analysis revealed that the viable/total bacterial cell ratio was 1.98–13.28%. This is the first study to provide important systematic insights into the microbiome of the CSS during assembly that describes the pre-launch microbial diversity of the space station. Our findings revealed the following. (1) Bacillus strains and staff activities should be considered major concerns for future biological safety. (2) Autotrophic and multi-resistant microbial communities were widespread in the AIT environment. Although harsh cleaning methods reduced the number of microorganisms, stress-resistant strains were not completely removed. (3) Sampling, storage and analytical methods for the space station were thoroughly optimized, and are expected to be applicable to low-biomass environments in general. Microbiology-related future works will follow up to comprehensively understand the changing characteristics of microbial communities in CSS. [ABSTRACT FROM AUTHOR]

We investigated the bacterioplankton abundance, community composition and the associated Vibrio clades of natural seawater in Bohai Sea coastal waters. Seawater samples (10 L in triplicate) were collected at 0.5, 3, and 5 m depths near the coastal aquaculture zone of the Bohai Sea on May 12, 2016. Real-time PCR and 16S rRNA gene amplicon high-throughput sequencing methods were employed by which 485 operational taxonomic units (OTUs) at a 97% sequence similarity level were generated. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes were the most abundant groups, accounting for 49.5%, 23.5%, and 18.9% of the total assemblage, respectively. Obvious variations in Pseudoalteromonas, Vibrio, and Octadecabacter, which were the most abundant genera, could be observed among different samples. Notably, the results of Vibrio-specific real-time PCR indicated that Vibrio had extremely high 16S rRNA gene copy numbers. The 16S rRNA gene sequencing results across all the samples also indicated that they occupied a large proportion of the total assemblage. Both the alpha diversity and major bacterioplankton group Pseudoalteromonas had significant correlations with the concentration of PO43−. Overall, studies on bacterioplankton communities with highly abundant Vibrio clades can provide interesting insight into the microbial function and health assessment of the Bohai Sea coastal ecosystem. [ABSTRACT FROM AUTHOR]

Restoration of the American chestnut (Castanea dentata) is underway using backcross breeding that confers chestnut blight disease resistance from Asian chestnuts (most often Castanea mollissima) to the susceptible host. Successful restoration will depend on blight resistance and performance of hybrid seedlings, which can be impacted by below-ground fungal communities. We compared fungal communities in roots and rhizospheres (rhizobiomes) of nursery-grown, 1-year-old chestnut seedlings from different genetic families of American chestnut, Chinese chestnut, and hybrids from backcross breeding generations as well as those present in the nursery soil. We specifically focused on the ectomycorrhizal (EcM) fungi that may facilitate host performance in the nursery and aid in seedling establishment after outplanting. Seedling rhizobiomes and nursery soil communities were distinct and seedlings recruited heterogeneous communities from shared nursery soil. The rhizobiomes included EcM fungi as well as endophytes, putative pathogens, and likely saprobes, but their relative proportions varied widely within and among the chestnut families. Notably, hybrid seedlings that hosted few EcM fungi hosted a large proportion of potential pathogens and endophytes, with possible consequences in outplanting success. Our data show that chestnut seedlings recruit divergent rhizobiomes and depart nurseries with communities that may facilitate or compromise the seedling performance in the field. [ABSTRACT FROM AUTHOR]

Purpose: Ammonia oxidation is the rate-limiting step in nitrification. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the key drivers of the nitrogen cycle. Chinese milk vetch (MV) has the potential to substitute for part of chemical fertilizer, but it remains unclear how MV is able to replace N fertilizer. The purpose of this study was to investigate the rice yield, soil properties, potential nitrification activity (PNA), abundances, and community structures of ammonia oxidizers in a paddy soil under MV combinations of different rates of chemical fertilizer. Materials and methods: This study was conducted at a long-term Experimental Station of the Fujian Academy of Agricultural Sciences, Fuzhou, China. The treatments included a control (without fertilization), NPK (chemical fertilizer), MF80 (MV plus 80% NPK), MF60 (MV plus 60% NPK), and MF40 (MV plus 40% NPK). Soil samples were collected after the rice harvest. We determined the soil physico-chemical properties and PNA. The abundances and community structures of AOB and AOA were assessed using their ammonia monooxygenase (amoA) genes. Quantitative PCR was used to determine the gene abundance, and Illumina Miseq sequencing was used to explore the diversity of AOB and AOA. Results and discussion: MV significantly increased the soil organic matter and PNA in comparison to the NPK. The available nitrogen content was higher in the MV treatments than in the control and NPK. Compared to the NPK, the application of MV increased the AOB abundance but decreased that of AOA. The abundance of AOA was higher in the control and NPK, but lower in the MV treatments than that of AOB. PNA was significantly positively correlated with the AOB abundance. The primary dominant OTU of the AOB group was Nitrosospira. MV significantly affected the AOB community, while no impact on the AOA community was observed. Principal coordinate analysis showed that the MV treatments were significantly distinct from those of the control and NPK. Redundancy analysis indicated that the soil OM, TN, AN, pH, and PNA were significantly correlated to the AOB community structure. Conclusions: This study demonstrated that MV combined with reduced chemical fertilizer would contribute to the improvement of soil fertility and PNA, resulting in rice yield comparable to that of the NPK. MV had a stronger effect on the AOB community than did chemical fertilizer. AOB played a more important role than AOA in the ammonia oxidation in this soil. [ABSTRACT FROM AUTHOR]

Aims: Heilongjiang Province in China experiences extremely cold weather, and its soil is saline-alkaline. Salinity and alkalinity severely restrain the growth of maize. Although Trichoderma treatment has been extensively evaluated as a promising strategy to improve soil quality, its impact on the bacterial community and physiochemical properties of this soil type is unclear.Methods: In the current study, different amounts of Trichoderma were used in field experiments in the Heilongjiang Province for two consecutive years. High-throughput sequencing was used to analyse the impact of Trichoderma on bacterial diversity in maize rhizosphere soils. Changes in root growth, crop yield, and soil physicochemical properties were also monitored.Results: Treatment with Trichoderma increased the overall abundance of bacteria in soil and affected the bacterial community structure in the rhizosphere soil. It also significantly increased the relative abundance of beneficial bacterial genera, including Nitrospira and Sphingomonas. Bacteria from the genus Stenotrophomonas were identified exclusively in Trichoderma treatment groups. Pearson's correlation analysis revealed that changes in soil bacterial community composition were closely related to soil characteristics such as the pH, organic matter, and total nitrogen, and were highly correlated with Trichoderma treatment. Trichoderma treatment increased crop yield by 4.87-12.41%.Conclusions: These findings suggest that Trichoderma treatment remarkably improves enzyme activity and nutrient content in soil; optimizes the microecological environment of the rhizosphere soil of maize; alleviates bacterial community degeneration in saline-alkaline soil from cold-region; and promotes the growth of maize plants, ultimately increasing crop yield.Relationships among bacterial diversity composition and soil and plant properties in the rhizosphere soil under Trichoderma treatments. [ABSTRACT FROM AUTHOR]

Uveitis (UVT), an inflammatory disease of the eye significantly contributes to vision impairment and blindness. Uveitis is associated with systemic infectious and autoimmune diseases, but in most cases, the aetiology remains unidentified. Dysbiosis in the gut microbiome has been implicated in autoimmune diseases, inflammatory diseases, cancers and mental disorders. In a mice model of autoimmune UVT, it was observed that manipulating the gut microbiome reduces the inflammation and disease severity. Further, alterations in the bacterial gut microbiome and their metabolites were reported in UVT patients from a Chinese cohort. Hence, it is worth comparing the bacterial gut microbiome of UVT patients with that of healthy controls (HC) to ascertain whether dysbiosis of the gut microbiome has implications in UVT. Our analyses showed reduced diversity of several anti-inflammatory organisms including Faecalibacterium, Bacteroides, Lachnospira, Ruminococcus and members of Lachnospiraceae and Ruminococcaceae families, and enrichment of Prevotella (proinflammatory) and Streptococcus (pathogenic) OTUs in UVT microbiomes compared to HC. In addition, decrease in probiotic and antibacterial organisms was observed in UVT compared to HC microbiomes. Heatmap and PCoA plots also indicated significant variations in the microbiomes of UVT versus HC. This is the first study demonstrating dysbiosis in the gut bacterial communities of UVT patients in an Indian cohort and suggests a role of the gut microbiome in the pathophysiology of UVT. [ABSTRACT FROM AUTHOR]

Main conclusion: An interesting AMF colonization microcosm has been detected in the roots of Pancratium maritimum (sea daffodil). Both sequencing techniques (Sanger and NGS) have been used for AMF characterisation, showing a balanced trade-off between pros and cons.By Sanger and next generation sequencing of rRNA nuclear molecular markers (SSU-ITS-LSU and ITS2, respectively), the presence of AMF communities in the roots of P. maritimum was evaluated. Our results shed light on the presence of AMF in sea daffodil and the diversity of assemblages of AMF detected after Sanger sequencing of the SSU-ITS-LSU marker is much higher than that determined following NGS sequencing of ITS2 alone. [ABSTRACT FROM AUTHOR]

Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial in which a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO 2 concentration of the host plant was observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread into higher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Tidal flats are extremely dynamic habitats in several environmental parameters, which enforces severe selection on their microbial inhabitants. Despite good knowledge of the species present, little is known about the temporal dynamics of their communities. Aim of the study was the investigation of cyanobacterial populations in intertidal flats of the German Wadden Sea and their seasonal- and sediment-type related dynamics of community composition based on next generation sequencing of 16S rRNA fragments. Most of the detected cyanobacterial taxa were present throughout the year, but with changing distribution patterns in different sediment types suggesting migration processes between sediment types during the year. Seasonal as well as tidal changes of environmental conditions and the heterogeneity of the study site concerning grain-size and related parameters created a temporally and spatially highly dynamic ecosystem. Development of microbial mats and community composition was mainly influenced by seasons. The annual mat growth started in spring and reached its maximum in late summer with highest richness as well-stabilized laminated structure. Different grain-sizes provided alternative niches for present taxa when conditions change. Coleofasciculus, Hydrocoleum, and Lyngbya were dominating genera in all sediment types. Βeta diversity of seasonal groups was influenced by the interval between sampling dates. [ABSTRACT FROM AUTHOR]

Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps. [ABSTRACT FROM AUTHOR]

While the acquisition of drug resistance is often accompanied by fitness costs, Mycobacterium tuberculosis has developed mechanisms to overcome these costs in the form of compensatory mutations. In an attempt to dissect strain-specific differences in biological fitness, 10 M. tuberculosis genomes, representing F15/LAM4/KZN, Beijing, F11 and F28 genotypes were sequenced on the Illumina MiSeq platform. Drug-susceptible F15/LAM4/KZN strains differed by 43 SNPs, demonstrating that heterogeneity exists even among closely-related strains. We found unique, nonsynonymous single-nucleotide polymorphisms (SNPs) in the sigA and grcC1 genes of multidrug resistant (MDR) and XDR F15/LAM4/KZN strains, respectively. The F28 MDR strain harboured a novel ubiA mutation in combination with its embB M306I mutation, which may be related to ethambutol resistance. In addition, it possessed a low-frequency rpoC mutation, suggesting that this strain was in the process of developing compensation. In contrast, no compensatory mutations were identified in Beijing and F11 MDR strains, corroborating its low in vitro fitness. Clinical strains also harboured unique SNPs in a number of important genes associated with virulence, highlighting the need for future studies which examine the correlation of genetic variations with phenotypic diversity. In summary, whole-genome sequencing revealed the presence of fitness-compensatory mutations in F15/LAM4/KZN and F28 genotypes which predominate in MDR and/or extensively drug resistant (XDR) forms in KwaZulu-Natal, South Africa. [ABSTRACT FROM AUTHOR]

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation. [ABSTRACT FROM AUTHOR]

Anode chamber of a dual chamber microbial fuel cell (MFC) having raw landfill leachate was inoculated with consortium of sulphate-reducing bacteria (SRB) and sulphide-oxidizing bacteria (SOB) to study the phylogenetic architecture, function and mutualism of anolyte community developed in the reactor. Enriched microbial community was analysed with the help of Illumina MiSeq and indicated the dominance of Firmicutes (41.4%), Clostridia (36.4%) and Clostridium (12.9%) at phylum, class and genus level, respectively. Clostridium was associated with fermentation as well as transfer of electrons to the electrode mediated by ferredoxin. Desulfovibrio (6.7%), Aeromonas (6.6%) and Tetrathiobacter (9.8%) were SRB-SOB associated with direct electron transfer to the electrode. Community analysis disclosed a syntrophic association among novel Firmicutes and Proteobacteria species for bioelectricity generation and degradation of organic matter. Complete removal of chemical oxygen demand was observed from landfill leachate within 3 days of inoculation. Lower oxidative slope and polarization resistance revealed from Tafel analysis backed the feasibility of electron transfer from microbes to anodic electrode and thus development of efficient anode-respiring community. Following enrichment and stabilization of the anodic community, maximum power density achieved was 9.15 W/m and volumetric current density was 16.17 A/m. Simultaneous feeding with SRB-SOB and landfill leachate led to the enrichment of a novel, mutually interdependent microbial community capable of synchronized bioremediation of effluents rich in carbon, sulphate, nitrate and aromatic compounds. [ABSTRACT FROM AUTHOR]

Chinese Mongolian sheep are an important ruminant raised for wool and meat production. However, little is known about the microbiota of the gastrointestinal tract (GIT) of Chinese Mongolian sheep. To increase our understanding of the microbial community composition in the GIT of Chinese Mongolian sheep, microbiota of five sheep is investigate for the first time using the Illumina MiSeq platform. High microbial diversity was obtained from the GIT, and the microbiota exhibited a higher biodiversity in the stomach and large intestine than in the small intestine. Firmicutes (44.62%), Bacteroidetes (38.49%), and Proteobacteria (4.11%) were the three most abundant phyla present in the GIT of the sheep. The present study also revealed the core genera of Prevotella, Bacteroides, Ruminococcus, Oscillospira, Treponema, and Desulfovibrio in the GIT. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States indicated that the metabolic pathway related to carbohydrate metabolism was the richest in the sheep GIT. In addition, a series of metabolic pathways related to plant secondary metabolism was most abundant in the stomach and large intestine than in the small intestine. Overall, the present study provides insight into the microbial community composition in GIT of the Chinese Mongolian sheep which is highly diverse and needs to be studied further to exploit the complex interactions with the host. [ABSTRACT FROM AUTHOR]

Peatlands play an important role in global climate change through sequestration of atmospheric CO. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO concentrations). Peat litterbags were placed in mesocosms, and fungal communities in litterbags were monitored over 12 months to assess the impacts of climate change variables on peat-inhabiting fungi. Changes in fungal richness, diversity, and community composition were assessed using Illumina MiSeq sequencing of ribosomal DNA (rDNA). While general fungal richness reduced under warming conditions, Ascomycota exhibited higher diversity under increased temperature treatments over the course of the experiment. Both increased temperature and lowered water table position drove shifts in fungal community composition with a strong positive effect on endophytic and mycorrhizal fungi (including one operational taxonomic unit (OTU) tentatively identified as Barrenia panicia) and different groups of saprotrophs identified as Mortierella, Galerina, and Mycena. These shifts were observed during a predicted degradative succession in the decomposer community as different carbon substrates became available. Since fungi play a central role in peatland communities, increased abundances of saprotrophic fungi under warming conditions, at the expense of reduced fungal richness overall, may increase decomposition rates under future climate scenarios and could potentially aggravate the impacts of climate change. [ABSTRACT FROM AUTHOR]

This study evaluated the effect of inorganic mercury (Hg) on bacterial community and diversity in different soils. Three soils-neutral, alkaline and acidic-were spiked with six different concentrations of Hg ranging from 0 to 200 mg kg and aged for 90 days. At the end of the ageing period, 18 samples from three different soils were investigated for bacterial community structure and soil physicochemical properties. Illumina MiSeq-based 16s ribosomal RNA (rRNA) amplicon sequencing revealed the alteration in the bacterial community between un-spiked control soils and Hg-spiked soils. Among the bacterial groups, Actinobacteria (22.65%) were the most abundant phyla in all samples followed by Proteobacteria (21.95%), Bacteroidetes (4.15%), Firmicutes (2.9%) and Acidobacteria (2.04%). However, the largest group showing increased abundance with higher Hg doses was the unclassified group (45.86%), followed by Proteobacteria. Mercury had a considerable negative impact on key soil functional bacteria such as ammonium oxidizers and nitrifiers. Canonical correspondence analysis (CCA) indicated that among the measured soil properties, Hg had a major influence on bacterial community structure. Furthermore, nonlinear regression analysis confirmed that Hg significantly decreased soil bacterial alpha diversity in lower organic carbon containing neutral and alkaline soils, whereas in acidic soil with higher organic carbon there was no significant correlation. EC values obtained by a nonlinear regression analysis indicated that Hg significantly decreased soil bacterial diversity in concentrations lower than several guideline values. [ABSTRACT FROM AUTHOR]

Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [ Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition. [ABSTRACT FROM AUTHOR]

The mammalian gastrointestinal (GI) microbiome, which plays indispensable roles in host nutrition and health, is affected by numerous intrinsic and extrinsic factors. Among them, antibiotic (ATB) treatment is reported to have a significant effect on GI microbiome composition in humans and other animals. However, the impact of ATBs on the GI microbiome of free-ranging or even captive great apes remains poorly characterized. Here, we investigated the effect of cephalosporin treatment (delivered by intramuscular dart injection during a serious respiratory outbreak) on the GI microbiome of a wild habituated group of western lowland gorillas ( Gorilla gorilla gorilla) in the Dzanga Sangha Protected Areas, Central African Republic. We examined 36 fecal samples from eight individuals, including samples before and after ATB treatment, and characterized the GI microbiome composition using Illumina-MiSeq sequencing of the bacterial 16S rRNA gene. The GI microbial profiles of samples from the same individuals before and after ATB administration indicate that the ATB treatment impacts GI microbiome stability and the relative abundance of particular bacterial taxa within the colonic ecosystem of wild gorillas. We observed a statistically significant increase in Firmicutes and a decrease in Bacteroidetes levels after ATB treatment. We found disruption of the fibrolytic community linked with a decrease of Ruminoccocus levels as a result of ATB treatment. Nevertheless, the nature of the changes observed after ATB treatment differs among gorillas and thus is dependent on the individual host. This study has important implications for ecology, management, and conservation of wild primates. [ABSTRACT FROM AUTHOR]

Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community. [ABSTRACT FROM AUTHOR]

The silkworm ( Bombyx mori L.) is an ideal model of Lepidoptera. However, the diversity and function of the intestinal microbiota in the gut of silkworm remain largely unknown. Changes in the intestinal microecology in fluoride-resistant strain T6 and fluoride-susceptible strain 734 of the silkworm in response to fluoride exposure were investigated. T6 and 734 were treated with 200 mg/kg fluoride (designated as T6-T and 734-T groups) and deionized water (designated as T6-C and 734-C groups). Culture-dependent approach revealed that the numbers of intestinal bacteria in the 734-T group significantly decreased compared with that in the 734-C group (4.8 ± 0.6 × 10 CFU/mL vs. 7.5 ± 0.7 × 10 CFU/mL; P < 0.05). Analyses of the intestinal content pH showed that the pH decreased in the 734-T group only. Additionally, SCFA concentrations significantly decreased in both treatment groups compared with the control groups. High-throughput sequencing indicated that the intestinal microbiota in the 734-T group was significantly more diverse than those in the other groups. The bacterial community was composed of two dominant groups ( Firmicutes and Proteobacteria). Principal component analyses revealed a significant difference in the composition of the intestinal microbiota in the 734-T group compared with those in the other groups. Thaumarchaeota and Euryarchaeota were more abundant in the 734-T group, but they were less abundant in the other groups. This study enhances our understanding about the diversity and function of silkworm intestinal microbiota in response to fluoride exposure among silkworm strains with diverse resistance. [ABSTRACT FROM AUTHOR]

The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10-10, 10, and 10-10 CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples. [ABSTRACT FROM AUTHOR]

It has been demonstrated that an anaerobic digestion process cannot attain an efficient removal of several amino acids, with methionine being one of the most persistent of these. Thus, the effect that methionine amino acid has over the partial-nitritation process with fixed-biofilm configuration in terms of performance and bacterial community dynamics has been investigated. With respect to the performance with no addition, 100 mg/L methionine loading decreased ammonium oxidation efficiency in 60 % and 100 % at concentrations of 300 and 500 mg/L methionine, respectively. Bacterial biomass sharply increased by 30, 65, and 230 % with the addition of 100, 300, and 500 mg/L methionine, respectively. Bacterial community analysis showed that methionine addition supported the proliferation of a diversity of heterotrophic genera, such as Lysobacter and Micavibrio, and reduced the relative abundance of ammonium oxidizing genus Nitrosomonas. This research shows that the addition of methionine affects the performance of the partial-nitritation process. In this sense, amino acids can pose a threat for the of partial-nitritation process treating anaerobic digester supernatant at full-scale implementation. [ABSTRACT FROM AUTHOR]

The main aim of the study was to assess the gradient distribution and composition diversity of microbial taxa using a spatial scale with physicochemical heterogeneity between reclamation area and non-reclamation area. The grid method was utilized to set the sample belt and sample square. The Illumina MiSeq platform was used to study the gradient distribution of rhizosphere bacteria in reclamation and non-reclamation areas. Operational taxonomic units were used to measure bacterial relative abundance. The analysis results showed salt concentration can effect on differences in bacterial relative abundance and composition diversity due to a variable in the rhizosphere soil. Bacterial relative abundance in reclamation area was significantly lower than that in non-reclamation area. The bacterial community composition showed a statistically significant to spatial variability. Some bacterial phyla exit in the whole study area, out of accordance with salinity control. It means that the composition of bacterial community was varied for the environment disturbance, but it was not unique correlated to environment factor. Anaerolinea genus has significantly positive correlation with salinity. It indicated that Anaerolinea genus can provide an indicator to response the environment change. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25 % of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7 % in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85 %, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99 % for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions. [ABSTRACT FROM AUTHOR]

Rhizosphere and root-associated microbial communities are known to be related to soil-borne disease and plant health. In the present study, the microbial communities in rhizosphere soils and roots of both healthy and diseased Panax notoginseng were analyzed by high-throughput sequencing of 16S rRNA for bacteria and 18S rRNA internal transcribed spacer for fungi, to reveal the relationship of microbial community structure with plant health status. In total, 5593 bacterial operational taxonomic units (OTUs) and 963 fungal OTUs were identified in rhizosphere soils, while 1794 bacterial and 314 fungal OTUs were identified from root samples respectively. Principal coordinate analysis separated the microbial communities both in the rhizosphere soils and roots of diseased P. notoginseng from healthy plants. Compared to those of healthy P. notoginseng, microbial communities in rhizosphere soils and roots of diseased plants showed a decrease in alpha diversity. By contrast, bacterial community dissimilarity increased and fungal community dissimilarity decreased in rhizosphere soils of diseased plants, while both bacterial and fungal community dissimilarity in roots showed no significant difference between healthy and diseased plants. Redundancy analysis at the phylum level showed that mycorrhizal colonization and soil texture significantly affected microbial community composition in rhizosphere soils, whereas shoot nutrition status had a significant effect on microbial community composition in root samples. Our study provided strong evidence for the hypothesis that microbial diversity could potentially serve as an indicator for disease outbreak of medicinal plants, and supported the ecological significance of microbial communities in maintaining plant healthy and soil fertility. [ABSTRACT FROM AUTHOR]

Background and aims: It has frequently been shown that plants interact with soils to shape rhizosphere microbiomes. However, previous work has not distinguished between effects of soil properties per se, and effects attributable to the resident microbial communities of those soils. We aimed to test whether differences in the structure of bulk soil microbial communities, within a given soil type, would carry over to impact the structure of the rhizosphere microbial community. Methods: We used repeated chemical amendments to develop divergent bulk soil microbial community starting points from which rhizosphere development proceeded. Additionally, we contrasted rhizosphere microbiomes associated with two different cultivars of corn ( Zea mays). Results: A wide range of bacterial and archaeal taxa responded to chemical resource amendments, which reduced bulk soil microbiome diversities. Corn genotypes P9714XR and 35F40 had largely similar impacts on rhizosphere microbiome development, although significant differences were evident in select treatments. Notably, in cases where resource amendments altered bulk soil microbial community composition, legacy effects persisted into the rhizosphere. Conclusions: Our results suggest that rhizosphere microbial communities may develop into different states depending on site history and prior selective events. This work advances our understanding of soil microbiome dynamics and responsiveness to change in the form of simple resource amendments and the development of the rhizosphere. [ABSTRACT FROM AUTHOR]

The present paper aims to explore the rhizospheric bacterial communities associated with Saccharum arundinaceum grown on organometallic pollutants-rich hazardous distillery sludge. The sequence analysis of 16S rRNA V3–V4 hypervariable region with Illumina MiSeq platform showed 621,897 OTUs derived from rhizospheric and non-rhizospheric distillery sludge samples out of 1,191,014 and 901,757 sequences read, respectively. The major phyla detected in rhizospheric sludge sample were Proteobacteria (50%), Bacteriodetes (33%), Firmicutes (5%) Gemmatimonadetes (2%), Chloroflexi (2%), and Tenericutes (2%). The dominant three genera were detected as Rheinheimera (21%), Sphingobacterium (17%), and Idiomarina (8%). In addition, other minor genera such as uncultured Bacillus (4%), Acidothermus (4%), Bacillus (3%), Pseudomonas (2%), Flavobacterium (2%), uncultured bacterium (2%), Parapedobacter (2%), Alcanivorax (2%), Acholeplasma (2%), Hyphomonas (1%), and Aquamicrobium were also detected (1%) in rhizospheric sludge. Our results suggested that rhizospheric bacterial communities associated with S. arundinaceum were substantially different in richness, diversity, and relative abundance of taxa compared to non-rhizospheric sludge. Further, the comparative organic pollutant analysis from non-rhizospheric and rhizospheric sludge samples through GC–MS analysis revealed the disappearance of few compounds and generation of some compounds as new metabolic products by the activity of rhizospheric bacterial communities. The results of this study will be helpful in understanding the role of rhizospheric bacterial communities responsible for degradation and detoxification of complex organometallic waste and, thus, can help in designing appropriate phytoremediation studies for eco-restoration of polluted sites. [ABSTRACT FROM AUTHOR]