Number Of Operational Taxonomic Units Research Articles

Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA

Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.

Impact of water depth and flow velocity on organic matter removal and nitrogen cycling in floating constructed wetlands

The configuration of water depth (WD) and flow velocity (FV) in floating constructed wetlands (FCWs) reflects the complex interactions between hydraulic conditions and wastewater treatment performance. Properly configuring hydraulic conditions can optimize performance. This study explored the removal and degradation of organic matter and nitrogen (N) in FCWs with three different WDs (50 cm (SD), 70 cm (MD), and 95 cm (DD)) under four FV conditions (0, 0.3, 1.0, and 1.5 m/d). It also analyzed the regulatory effects of hydraulic conditions on microbial community structure to provide new insights for configuring hydraulic conditions in FCWs. The results indicate that variations in WD and FV do not significantly affect COD removal (p > 0.05), with removal efficiency (RE) consistently reaching 90 % across all conditions. However, hydraulic conditions do influence the degradation rate (k) of COD, with increased FV enhancing the k in MD and DD. In contrast, WD significantly impacts the removal of NH4+−N (p < 0.05), with RE in SD exceeding 80 % across all four FVs. The primary reason is that increased WD reduced the abundance of nitrifying bacteria (Nitrosomonas and Nitrospira) and functional genes (hao and pmoABC-amoABC). Meanwhile, increased WD and FV significantly enriched the denitrifying bacteria genera (such as Massilia, Bacillus, Ensifer, and Rhodobacter) and certain functional genes (nap and nir), favoring the denitrification process and enhancing the dissimilatory nitrate reduction to ammonium (DNRA) process. Furthermore, microbial community diversity, richness, and the number of operational taxonomic units (OTUs) were highest in SD, but decreased with increased WD. This is mainly related to changes in oxygen (O2) transmission and nutrient concentration. These findings help us understand the mechanisms by which hydraulic regulation affects the removal of organic matter and N in FCWs. They also propose potential solutions from a hydraulics perspective to enhance N removal.

Extreme Temperatures Reduce Copepod Performance and Change the Relative Abundance of Internal Microbiota

ABSTRACTCopepods are one of the most abundant invertebrate groups in the seas and oceans and are a significant food source for marine animals. Copepods are also particularly sensitive to elevated temperatures. However, it is relatively unknown how the internal microbiome influences copepod susceptibility to warming. We addressed this fundamental knowledge gap by assessing key life history traits (survival, development, and reproduction) and changes in the internal microbiome in the tropical calanoid copepod Acartia sp. in response to warming (26°C, 30°C, and 34°C). Copepod microbiomes were analyzed using high throughput DNA sequencing of V1–V9 of 16S rRNA hypervariable regions. Copepod performance was better at 30°C than at 26°C, as indicated by faster development, a higher growth rate, and fecundity. However, these parameters strongly decreased at 34°C. We recorded 1,262,987 amplicon sequence reads, corresponding to 392 total operational taxonomic units (OTUs) at 97% similarity. Warming did not affect OTU numbers and the biodiversity indices, but it substantially changed the relative abundance of three major phyla: Proteobacteria, Actinobacteria, and Bacteroidota. The thermophilic and opportunistic Proteobacteria and Bacteroidota increased under extreme temperatures (34°C) while Actinobacteria abundance was strongly reduced. Changes in the relative abundance of these bacteria might be related to reduced copepod growth, survival, and reproduction under extreme temperatures. Profiling the functional role of all internal bacterial groups in response to the temperature change will fundamentally advance our mechanistic understanding of the performance of tropical copepods and, more generally, marine invertebrates to a warming climate.

The Effect of Spatio‐Temporal Sampling and Biological Replication on the Detection of Kelp Forest Fish Communities Using eDNA Metabarcoding

ABSTRACTEnvironmental DNA (eDNA) metabarcoding surveys can support the acquisition of extensive biodiversity data to support ecosystem monitoring and conservation actions. However, the optimization of eDNA metabarcoding project design is essential to capture spatio‐temporal heterogeneity of eDNA signals and maximize diversity detection. In this study, we developed a system‐specific approach to detect fish communities in kelp forests, by analyzing fine‐scale spatio‐temporal patterns in eDNA signals at two sites along the South African coastline, as well as testing the effect of biological replication and pooling of replicates on species detection. At each site, samples were collected at two stations along the shoreline at two depth zones, and this was repeated at two time points (24 h apart). We detected 113 operational taxonomic units (OTUs) across 32 families, but fewer than 20% of OTUs could be assigned to species, indicating that barcode reference libraries need to be drastically improved. We detected significant differences in communities across small spatial scales (&lt; 600 m) and time points, suggesting that to best capture a site's diversity patterns, samples should be collected at multiple points and times within at least 24 h. To detect ~80% of the fish community, including some low abundance species, a minimum of four samples appear sufficient. In addition, a higher number of OTUs (76 vs. 65) were found in individual replicates than in any of the pools. However, pooling samples prior to sequencing can still detect valuable broad‐scale biodiversity patterns for monitoring and can offset the decrease in data resolution with the benefit of accumulating comprehensive data from increased sampling efforts over time. As a pilot investigation into how best to maximize kelp forest‐associated fish communities, this study provides a basis for optimizing sampling design for coastal eDNA‐based surveys in southern Africa and strengthens the development of long‐term eDNA monitoring programs to better support conservation and management actions.

Soil pathogenic fungal groups and soil nutrient cycling under land use practices in Liupanshan Mountain in China

AbstractDifferent land‐use practices in temperate forests strongly affect soil quality and soil microbial communities, whereas the assembly and interactions of soil functional fungal communities provide positive feedback. Therefore, the effects of forest ecosystem degradation on the composition of functional soil fungal community and soil nutrient cycling are of particular importance. We studied forest ecosystems in the Liupanshan Mountains in the northwestern part of the Loess Plateau and analyzed the relationship of soil fungal community and soil nutrient cycling under different land use practices (natural forest [NF], plantation forest, and farmland [FL]). The results showed that soil pH and electrical conductivity were the highest in FL, whereas the soil carbon cycle index and nitrogen cycle index decreased. The soil total phosphorus content did not change significantly with an increase in available phosphorus content. The change from NF to FL significantly increased the number of operational taxonomic units, diversity, and richness of soil fungal communities. The composition of the soil fungal communities was also strongly influenced by carbon and nitrogen cycle indices. In addition, FL reclamation increased the complexity of the soil microorganism co‐occurrence network, and the interrelationships between soil functional fungal community were enhanced. Pathogenic fungal communities were enriched in FLs, and their relative abundance was significantly regulated by environmental factors such as pH and the ratio of nitrogen to phosphorus. The soil pathogenic fungal community affected carbon and nitrogen cycle indices to varying degrees.

Microbial regulatory mechanisms of disease-resistant tobacco varieties in the prevention and control of bacterial wilt disease

Bacterial wilt disease poses a significant threat to the production and quality of tobacco. Disease-resistant varieties of tobacco are the primary means of preventing bacterial wilt, but the soil microbial mechanisms that alleviate this disease require further in-depth research. In our study, we analyzed the physicochemical and microbial properties of rhizosphere soil in four different disease-resistant varieties of tobacco. The treatments included: T1 (Chang Bo Huang; 100 % infection rate); T2 (Yun Yan 87; 80 % infection rate); T3 (K326; 50 % infection rate) and T4 (YAN YAN 97; 0 % infection rate). Our results showed that the T4 treatment improved the fresh biomass of tobacco by 35.42 % compared to the T1 treatment. In addition, a significant increase in soil pH and soil organic matter (SOM) from 4.98 and 1.24 % under T1 treatment to 5.86 and 1.38 % under T4 treatment, respectively. As the disease resistance of the tobacco variety improved was found, there was a noticeable upward trend in the number of operational taxonomic units (OTUs) in the rhizosphere soil, showing higher sensitivity compared to fungi. Additionally, rhizosphere soil from susceptible varieties exhibited higher levels of metabolites, resulting in the accumulation of acidic substances (6-aminopenicillanic acid, garcinia acid, and 4-decan-4-ylbenzenesulfonic acid). Moreover, these soil metabolites might have attracted certain pathogenic fungi (Monoblepharomycota), contributing to the spread of soil diseases. This study suggests that the rhizosphere soil of disease-resistant tobacco variety provides a better microecological environment which could inhibit accumulation of allelopathic substances and reduce the spread of bacterial wilt disease.

Multiple-trait genomic prediction for swine meat quality traits using gut microbiome features as a correlated trait.

Traits such as meat quality and composition are becoming valuable in modern pork production; however, they are difficult to include in genetic evaluations because of the high phenotyping costs. Combining genomic information with multiple-trait indirect selection with cheaper indicator traits is an alternative for continued cost-effective genetic improvement. Additionally, gut microbiome information is becoming more affordable to measure using targeted rRNA sequencing, and its applications in animal breeding are becoming relevant. In this paper, we investigated the usefulness of microbial information as a correlated trait in selecting meat quality in swine. This study incorporated phenotypic data encompassing marbling, colour, tenderness, loin muscle and backfat depth, along with the characterization of gut (rectal) microbiota through 16S rRNA sequencing at three distinct time points of the animal's growth curve. Genetic progress estimation and cross-validation were employed to evaluate the utility of utilizing host genomic and gut microbiota information for selecting expensive-to-record traits in crossbred individuals. Initial steps involved variance components estimation using multiple-trait models on a training dataset, where the top 25 associated operational taxonomic units (OTU) for each meat quality trait and time point were included. The second step compared the predictive ability of multiple-trait models incorporating different numbers of OTU with single-trait models in a validation set. Results demonstrated the advantage of including genomic information for some traits, while in some instances, gut microbial information proved advantageous, namely, for marbling and pH. The study suggests further investigation into the shared genetic architecture between microbial features and traits, considering microbial data's compositional and high-dimensional nature. This research proposes a straightforward method to enhance swine breeding programs for improving costly-to-record traits like meat quality by incorporating gut microbiome information.

Sequence analysis of microbiota in clinical human cases with diabetic foot ulcers from China

BackgroundDiabetic foot ulcers (DFU) seriously threaten the health and quality of life of patients. The microbiota is the primary reason for the refractory and high recurrence of DFU. This study aimed to determine the wound microbiota at different DFU stages. MethodsWound samples were collected from 48 patients with DFU and divided into three phases: inflammatory (I, n = 49), proliferation (P, n = 22), and remodeling (R, n = 19). The wound samples obtained at different stages were then subjected to 16S rRNA gene sequencing. The number of operational taxonomic units (OTUs) in the different groups was calculated according to the criterion of 97 % sequence similarity. The diversity of the microbiota differentially presented bacterial taxa at the phylum and genus levels, and important phyla and genera in the different groups were further explored. ResultsAfter sequencing, 3351, 925, and 777 OTUs were observed in groups I, P, and R, respectively, and 175 OTUs overlapped. Compared with the inflammatory stage, the α-diversity of wound microbiota at proliferation and remodeling stages was significantly decreased (P < 0.05). At the phylum level, Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were the dominant phyla, accounting for more than 90 % of all the phyla. At the genus level, Random Forest and linear discriminant analysis effect size analyses showed that Peptoniphilus, Lactobacillus, Prevotella, Veillonella, Dialister, Streptococcus, and Ruminococcus were the signature wound microbiota for the inflammatory stage; Anaerococcus, Ralstonia, Actinomyces, and Akkermansia were important species for the proliferation stage; and the crucial genera for the remodeling stage were Enterobacter, Pseudomonas, Sondgrassella, Bifidobacterium, and Faecalibacterium. ConclusionsThere were significant differences in the composition and structure of the wound microbiota in patients with DFU at different stages, which may lay a foundation for effectively promoting wound healing in DFU.

The Cellular Microbiome of Visceral Organs: An Inherent Inhabitant of Parenchymal Cells.

The cell is the basic unit of life. It is composed of organelles and various organic and inorganic biomolecules. Recent 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing studies have revealed the presence of tissue bacteria in both tumor and normal tissues. Recently, we found that the liver microbiome resided in hepatocytes. Here, we further report on the cellular microbiome in the parenchymal cells of visceral organs as inherent inhabitants. We performed 16S rRNA gene sequencing on visceral organs of male adult Sprague Dawley (SD) rats, pregnant rats, newborn rats, and fetuses and placentas; then, we performed fluorescence in situ hybridization and immunofluorescence in visceral organs. Furthermore, we performed Western blotting on nuclear and cytoplasmic extractions of visceral organs of SD rats and cell lines HepG2, Huh-7, Hepa1-6, and HSC-T6. A high abundance of 16S rRNA gene was detected in the visceral organs of male adult, pregnant, newborn, and fetal rats as well as their placentas. The number of operational taxonomic units (OTUs) of visceral bacteria was higher than that of the feces and ileum bacteria. Bacterial 16S rRNA, lipopolysaccharide (LPS), and lipoteichoic acid (LTA) were found in the parenchymal cells of visceral organs, as well as in HepG2, Huh-7, HSC-T6, and Hepa1-6 cells. LPS consistently appeared in the nucleus of cells, while LTA was mainly found in the cytoplasm. In conclusion, the cellular microbiome is an intrinsic component of cells. Gram-negative bacteria are located in the nucleus, and Gram-positive bacteria are located in the cytoplasm. This differs from the gut microbiome and may be inherited.

Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259–11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

An optimal combined slow-release nitrogen fertilizer and urea can enhance the decomposition rate of straw and the yield of maize by improving soil bacterial community and structure under full straw returning system.

Under a full straw returning system, the relationship between soil bacterial community diversity and straw decomposition, yield, and the combined application of slow-release nitrogen and urea remains unclear. To evaluate these effects and provide an effective strategy for sustainable agricultural production, a 2-year field positioning trial was conducted using maize as the research object. Six experimental treatments were set up: straw returning + no nitrogen fertilizer (S1N0), straw returning + slow-release nitrogen fertilizer:urea = 0:100% (S1N1), straw returning + slow-release nitrogen fertilizer:urea = 30%:70% (S1N2), straw returning + slow-release nitrogen fertilizer:urea = 60%:40% (S1N3), straw returning + slow-release nitrogen fertilizer:urea = 90%:10% (S1N4), and straw removal + slow-release nitrogen fertilizer:urea = 30%:70% (S0N2). Significant differences (p < 0.05) were observed between treatments for Proteobacteria, Acidobacteriota, Myxococcota, and Actinobacteriota at the jointing stage; Proteobacteria, Acidobacteriota, Myxococcota, Bacteroidota, and Gemmatimonadota at the tasseling stage; and Bacteroidota, Firmicutes, Myxococcota, Methylomirabilota, and Proteobacteria at the maturity stage. The alpha diversity analysis of the soil bacterial community showed that the number of operational taxonomic units (OTUs) and the Chao1 index were higher in S1N2, S1N3, and S1N4 compared with S0N2 at each growth stage. Additionally, the alpha diversity measures were higher in S1N3 and S1N4 compared with S1N2. The beta diversity analysis of the soil bacterial community showed that the bacterial communities in S1N3 and S1N4 were more similar or closely clustered together, while S0N2 was further from all treatments across the three growth stages. The cumulative straw decomposition rate was tested for each treatment, and data showed that S1N3 (90.58%) had the highest decomposition rate. At the phylum level, straw decomposition was positively correlated with Proteobacteria, Actinobacteriota, Myxococcota, and Bacteroidota but significantly negatively correlated with Acidobacteriota. PICRUSt2 function prediction results show that the relative abundance of bacteria in soil samples from each treatment differed significantly. The maize yield of S1N3 was 15597.85 ± 1477.17 kg/hm2, which was 12.80 and 4.18% higher than that of S1N1 and S0N2, respectively. In conclusion, a combination of slow-release nitrogen fertilizer and urea can enhance the straw decomposition rate and maize yield by improving the soil bacterial community and structure within a full straw returning system.

Heat stress has divergent effects on the milk microbiota of Holstein and Brown Swiss cows.

Heat stress (HS) is one of the pivotal causes of economic losses in dairy industries and affects welfare and performance, but its effect on milk microbiota remains elusive. It is also unclear if and how different breeds may cope with HS in sustaining productive performance. The objectives of this study were to compare a) the performance of 2 dairy breeds, namely Holstein and Brown Swiss, subjected to HS and b) the different effects of HS on the milk microbiota of the 2 breeds in thermal comfort conditions and HS. The study was carried out on 36 dairy cows, 18 per breed. The HS was induced by switching off the cooling system during a natural heat wave for 4 d. Besides the Temperature Humidity Index (THI), the animal stress was confirmed by measuring respiratory frequency and rectal temperature twice daily at 4 a.m. and 3 p.m. The HS differently impacted the 2 breeds. Rectal temperatures were higher in Holstein cows, while no changes in rectal temperature were found in Brown Swiss. Milk yield recording and sampling were performed during the morning milking of d 1 (at 4.00 a.m.) and afternoon milking of d 4 (at 5.00 p.m.). Productive parameters were also different: milk yield, fat-corrected milk, energy-corrected milk, protein and casein content, and renneting parameters were decreased in Holstein but remained unaffected in Brown Swiss. The HS also modified the milk microbiota of the 2 breeds differently. During HS, the Brown Swiss milk microbiota was richer (α diversity) than the Holstein one. Comparing the time points before and during HS within breeds showed that Brown Swiss milk microbiota was less affected by HS than Holstein's. Under the same thermal comfort condition, milk microbiota did not discriminate between Brown Swiss and Holstein. Consistently with α and β diversity, the number of operational taxonomic units (OTUs) at the genus level that changed their abundance during HS was higher in Holstein (74 OTUs) than in Brown Swiss (only 20 OTUs). The most significant changes in abundance affected Acinetobacter, Chryseobacterium, Cutibacterium, Enterococcus, Lactococcus, Prevotella-9, Serratia, and Streptococcus. In conclusion, the present report confirms and extends previous studies by demonstrating that Brown Swiss cows regulate their body temperature better than the Holstein breed. The relative thermal tolerance to HS compared with Holstein is also confirmed by changes in milk uncultured microbiota, which were more evident in Holstein than in Brown Swiss.

Metagenomic Assessment of Fungal Diversity in the Mangrove Sediments from North and Central Kerala, India

The fungal communities of mangrove sediments have wide ecological significance and are actively involved in nutrient recycling, decomposition of litter and degradation of recalcitrant substances. The present study focused on comparing the abundance, diversity and composition of fungal community in the sediments of two selected mangrove ecosystems of Kannur and Eranakulam districts of Kerala. Metagenomic analysis of the total sediment DNA was performed on an Illumina sequencing platform using fungal ITS primers. The number of Operational Taxonomic Units (OTUs) and the diversity indices showed that the Eranakulam mangrove sediments possessed higher fungal abundance, species richness and diversity than the mangrove sediments of Kannur. Ascomycota was most predominant phyla identified and a total of 11 classes, 20 orders, 34 families and 36 genera were obtained from the mangrove sediments. Talaromyces, which is not a commonly reported genus from Indian mangroves was the most prominent genera found in our study. The diversity heat map showed that 16 genera were exclusive to Eranakulam mangrove sediments while 5 genera were exclusive to Kannur samples. The metagenomics data of the mangrove sediments in our study revealed the presence of many fungal strains with vast biotechnological potential which can be further explored in the technology development.

Assessing the impacts of aquaculture on local fish communities using environmental DNA metabarcoding analysis

AbstractFish aquaculture potentially affects the local ecosystem through feed (leftovers) and feces. However, evaluation of its impacts on biodiversity, especially those of mobile organisms such as fish, is not straightforward. Here, we report a case study in which environmental DNA (eDNA) metabarcoding with MiFish universal primers for the 12S rRNA region of fish is used to detect and assess the impact of aquaculture on local fish communities. In Shizugawa Bay, Minamisanriku Town, Miyagi Prefecture, Japan, Oncorhynchus kisutch (coho salmon) is aquacultured in sea cages from November to July, but is absent from August to October. We conducted eDNA surveys in June, August, October, and December 2021 of water at depths of 5 m and 1 m above the bottom obtained from two sites, one approximately 100 m and the other approximately 2500 m from the nearest aquaculture site. The total number of operational taxonomic units (OTUs) detected was 122, with a maximum of 50 and a minimum of 10. With distance‐based redundancy analysis (dbRDA) and PERMANOVA applied to the eDNA‐based community compositional data, we detected a significant effect of the presence of O. kisutch aquaculture on fish biodiversity. The generalized linear model (GLM) applied to each detected OTUs indicated that the aquaculture was associated positively with Leucopsarion petersii (ice goby), and Oncorhynchus spp. and negatively with Chaenogobius annularis (forktongue goby). Environmental DNA metabarcoding surveys, combined with multivariate statics, are a promising tool to identify the dimension of biodiversity that human activity affects and would serve as a basic survey for sustainable use of the sea.

Cyanobacterial and moss biocrusts shape soil nematode community in dryland mountain ecosystems with increasing aridity

Soil nematodes are the most abundant animals on Earth and play critical roles in regulating numerous ecosystem processes, from enhancing primary productivity to mineralizing multiple nutrients. In dryland soils, a rich community of microphyte organisms (biocrusts) provide critical habitats for soil nematodes, but their presence is being threatened by increasing aridity induced by global climate change. Despite its importance, how types of biocrusts and aridity index influence soil nematode community in dryland mountain ecosystems remains largely unknown. To fill these knowledge gaps, we conducted a field survey with contrasting aridity indexes (0.2, 0.4, and 0.6) and three types of biocrusts (cyanobacterial, cyanobacterial-moss mixed, and moss crusts) in the topsoil (0–5 cm) from the northern Chinese Loess Plateau. We found that the abundance (number of individuals per gram of soil), richness (number of Operational Taxonomic Units; OTUs), and diversity (number of different species) of soil nematodes were remarkably higher under biocrusts than in bare soils, regardless of aridity index and types of biocrusts. Our results also showed that the same variables had the highest values in moss crusts compared to cyanobacterial and cyanobacterial-moss mixed crusts. Structural equation modelling further revealed that biocrust types and traits (i.e., biocrust thickness, chlorophyll content, shear force, and penetration resistance) are the most important factors associated with both nematode abundance and richness. Together, our findings indicate that biocrusts, especially moss cover, and less stressful aridity conditions favor soil nematodes community in dryland mountain regions. Such knowledge is critical for anticipating the distribution of these animals under climate change scenarios and, ultimately, the numerous ecosystem services supported by soil nematodes.

Do Concurrent Peri-Implantitis and Periodontitis Share Their Microbiotas? A Pilot Study.

The microbial compositions from concurrent peri-implant and periodontal lesions were compared, since the results reported in the literature on the etiological relationship between these oral pathologies are contradictory. Microbial compositions from nine patients were evaluated using Illumina MiSeq sequencing of 16S rRNA gene amplicons and Principal Components Analysis. Comparisons between the use of curettes or paper points as collection methods and between bacterial composition in both pathologies were performed. Paper points allowed the recovery of a higher number of bacterial genera. A higher bacterial diversity was found in peri-implantitis compared to periodontal samples from the same patient, while a greater number of operational taxonomic units (OTUs) were present in the corresponding periodontal samples. A higher abundance of oral pathogens, such as Porphyromonas or Treponema, was found in peri-implantitis sites. The opposite trend was observed for Aggregatibacter abundance, which was higher in periodontal than in peri-implantitis lesions, suggesting that both oral pathologies could be considered different but related diseases. Although the analysis of a higher number of samples would be needed, the differences regarding the microbial composition provide a basis for further understating the pathogenesis of peri-implant infections.

Comparison of DNA metabarcoding and microscopy in analysing planktonic protists from the European Arctic

In the era of climate change-related restructuring of planktonic protist communities, it is especially important to identify possible shifts in their taxonomic composition. While traditional microscopy-based morphological classification is time-consuming and requires experienced taxonomists, metabarcoding seems to substantially accelerate the determination of taxonomic composition. In this study, based on samples collected in summer 2019 from the West Spitsbergen Current, we analysed planktonic protists using both methods. Metabarcoding, based on high-throughput sequencing of the V4 region of the 18S rRNA gene, resulted in a much higher number of operational taxonomic units (OTUs) and sample diversity than microscopy, although the resolution of taxonomic identification ranged from species to phyla. Most morphology-based identification was performed at the species or genus level, additionally allowing us to include information about dominants and size fractions. The highest proportion of 45% shared taxa by both methods was recorded at the class level. The composition of dominant protists differed between the approaches, with most similarities being observed in Bacillariophyceae, for which two genera, Thalassiosira and Eucampia, were found to be the most abundant with both methods. For Dinophyceae, the most abundant representatives identified by microscopy were Gymnodinium spp., Prorocentrum minimum and Gonyaulax gracilis, while in the metabarcoding approach, most dinoflagellates were identified to the class level only. Given the different levels of accuracy of taxonomic determinations and possible biases in results connected to the chosen methodology, we advocate using an integrative taxonomic approach for the classification of planktonic protists based on the combination of microscopy and molecular methods.

Asymptomatic Enteric Virus Infections and Association with the Gut Microbiome in Rural Residents of Northern Laos.

Viral gastrointestinal infections are an important public health concern, and the occurrence of asymptomatic enteric virus infections makes it difficult to prevent and control their spread. This study aimed to determine the prevalence of and factors associated with asymptomatic enteric virus infection in adults in northern Laos. Fecal samples were collected from apparently healthy participants who did not report diarrhea or high fever at the time of the survey in northern Laos, and enteric viruses were detected using polymerase chain reaction (PCR) and reverse transcription (RT)-PCR. Individual characteristics, including the gut microbiome, were compared between asymptomatic carriers and noncarriers of each enteric virus. Of the participants (N = 255), 12 (4.7%) were positive for norovirus genogroup I (GI), 8 (3.1%) for human adenovirus, and 1 (0.4%) for norovirus GII; prevalence tended to be higher in less-modernized villages. Gut microbial diversity (evaluated by the number of operational taxonomic units) was higher in asymptomatic carriers of norovirus GI or human adenovirus than in their noncarriers. Gut microbiome compositions differed significantly between asymptomatic carriers and noncarriers of norovirus GI or human adenovirus (permutational analysis of variance, P <0.05). These findings imply an association between asymptomatic enteric virus infection and modernization and/or the gut microbiome in northern Laos.

Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam.

The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.

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.