Dominant Operational Taxonomic Units Research Articles

Microbiome Dynamics and Functional Composition in Coelopa frigida (Diptera, Coelopidae): Insights into Trophic Specialization of Kelp Flies

Coelopidae (Diptera), known as kelp flies, exhibit an ecological association with beached kelp and other rotting seaweeds. This unique trophic specialization necessitates significant adaptations to overcome the limitations of an algal diet. We aimed to investigate whether the flies’ microbiome could be one of these adaptive mechanisms. Our analysis focused on assessing composition and diversity of adult and larval microbiota of the kelp fly Coelopa frigida. Feeding habits of the larvae of this species have been subject of numerous studies, with debates whether they directly consume kelp or primarily feed on associated bacteria. By using a 16S rRNA metabarcoding approach, we found that the larval microbiota displayed considerably less diversity than adults, heavily dominated by only four operational taxonomic units (OTUs). Phylogenetic placement recovered the most dominant OTU of the larval microbiome, which is the source of more than half of all metabarcoding sequence reads, as an undescribed genus of Orbaceae (Gammaproteobacteria). Interestingly, this OTU is barely found among the 15 most abundant taxa of the adult microbiome, where it is responsible for less than 2% of the metabarcoding sequence reads. The other three OTUs dominating the larval microbiome have been assigned as Psychrobacter (Gammaproteobacteria), Wohlfahrtiimonas (Gammaproteobacteria), and Cetobacterium (Fusobacteriota). Moreover, we also uncovered a distinct shift in the functional composition between the larval and adult stages, where our taxonomic profiling suggests a significant decrease in functional diversity in larval samples. Our study offers insights into the microbiome dynamics and functional composition of Coelopa frigida.

Temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal communities with ontogenetic and phenological development in Prasophyllum (Orchidaceae).

Plant-fungus symbioses may experience temporal turnover during the host's ontogenetic or phenological development, which can influence the host plant's ecological requirements. This study investigates temporal turnover of Ceratobasidiaceae orchid mycorrhizal fungal (OMF) communities in Prasophyllum (Orchidaceae), asking if OMF communities are subject to temporal change due to orchid phenology or ontogeny. Roots of adult Prasophyllum frenchii, P. lindleyanum and P. sp. aff. validum from Australia were sampled between autumn and spring. Seed was sown in situ as 'baits' to explore the mycorrhizal associations of germinating protocorms, which were compared to OMF in roots of co-occurring adult plants. Culture dependent and independent sequencing methods were used to amplify the internal transcribed spacer and mitochondrial large subunit loci, with sequences assigned to Operational Taxonomic Units (OTUs) in phylogenetic analyses. Germination trials were used to determine if fungal OTUs were mycorrhizal. A persistent core of OMF associated with Prasophyllum, with Ceratobasidiaceae OMF dominant in all three species. Phenological turnover occurred in P. lindleyanum and P. sp. aff. validum, but not in P. frenchii, which displayed specificity to a single OTU. Ontogenetic turnover occurred in all species. However, phenological and ontogenetic turnover was typically driven by the presence or absence of infrequently detected OTUs in populations that otherwise displayed specificity to one or two dominant OTUs. Ex situ germination trials showed 13 of 14 tested OTUs supported seed germination in their host orchid, including eight OTUs that were not found in protocorms in situ. An understanding of OMF turnover can have practical importance for the conservation of threatened orchids and their mycorrhizal partners. However, frameworks for classifying OMF turnover should focus on OTUs important to the life cycle of the host plant, which we suggest are likely to be those that are frequently detected or functionally significant.

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean.

The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterialmetabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similarand were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.

Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum

BackgroundBacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2.ResultsOur results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere.ConclusionsThe study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.

Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient

Abstract Cycloclypeus carpenteri is one of the deepest living large benthic foraminifera. It has an obligatory relationship with diatom photosymbionts, and, in addition, houses a diverse prokaryotic community. Variations in the eukaryotic and prokaryotic endobiotic community composition might be key in allowing Cycloclypeus to occur in low light environments. We assessed the variability of the prokaryotic and eukaryotic communities associated with Cycloclypeus along a depth gradient from 50 to 130 m at two locations in the Federated States of Micronesia (Northwest Pacific) by metabarcoding of the 18S V9 rRNA region for eukaryotes and the 16S V3-V4 rRNA region for prokaryotes. We observed a single foraminiferal operational taxonomic unit (OTU), as well as a single dominant diatom OTU that was abundant in all sequenced specimens. Both the prokaryotic and the eukaryotic endobiotic communities (excluding the dominant diatom) changed with water depth and associated irradiance levels. We observed a distinct change in the prokaryotic community composition around 90–100 m water depth at Pohnpei, equivalent to ∼1% surface radiation. This change in microbial communities in the Cycloclypeus holobiont suggests a potential role of the associated microbial communities in accommodating differences in (micro)habitat, although we cannot exclude that the prokaryote community is to a large extent driven by their community composition in the ambient environment.

Predicting the multispecies solid-state vinegar fermentation process using single-cell Raman spectroscopy combined with machine learning

Microbial community is a key contributing factor for flavor formation in natural food fermentation. However, it is a challenge to maintain batch-to-batch uniformity during the fermentation process due to the diversity and variability of microbial community. A rapid detection of the structure and function of the microbial community in the whole fermentation process is of great importance for quality control of the final fermentation products. Firstly, we employed amplicon sequencing to target the dominant operational taxonomic units in the microbial community of Zhenjiang aromatic vinegar, a traditional cereal vinegar. Secondly, we isolated and created a Raman database for 13 dominant bacterial species from vinegar culture, enabling us to establish a logistic regression model with 96.4% accuracy in species classification. Finally, a Raman-fermentation phase regression model was established, achieving an R2 of 0.952, accurately determining the actual fermentation phase of vinegar. This study offers a new method for dynamics monitoring of microbial community, prediction of fermentation state, and decision of subsequent production operations in multi-species fermentation processes.

Contaminants of emerging concern reduction and microbial community characterization across a three-barrier advanced water treatment system

This research investigated the removal of contaminants of emerging concern (CECs) and characterized the microbial community across an advanced water treatment (AWT) train consisting of Coagulation/Flocculation/Clarification/Granular Media Filtration (CFCGMF), Ozone-Biological Activated Carbon Filtration (O3/BAC), Granular Activated Carbon filtration, Ultraviolet Disinfection, and Cartridge Filtration (GAC/UV/CF). The AWT train successfully met the goals of CECs and bulk organics removal. The microbial community at each treatment step of the AWT train was characterized using 16S rRNA sequencing on the Illumina MiSeq platform generated from DNA extracted from liquid and solid (treatment media) samples taken along the treatment train. Differences in the microbial community structure were observed. The dominant operational taxonomic units (OTU) decreased along the treatment train, but the treatment steps did impact the microbial community composition downstream of each unit process. These results provide insights into microbial ecology in advanced water treatment systems, which are influenced and shaped by each treatment step, the microbial community interactions, and their potential metabolic contribution to CECs degradation.

Startup performance and microbial composition of a pilot-scale rapid sand filter for the treatment of manganese-containing mine water

The inexpensive removal of soluble manganese [Mn(II)] from mine water that contains large quantities of Mn(II) should be prioritized given that large quantities of alkaline reagents are typically used in the chemical treatment of Mn-rich water from abandoned mines. Rapid sand filter (RSF) systems are widely used as a cost-effective technology in drinking water treatment processes to remove iron and Mn from groundwater. Here, we applied a pilot-scale RSF to treat mine water with a neutral pH and containing approximately 22 mg/L of Mn(II). Following a lag phase from its startup (day 1–day 26), Mn removal rates increased to approximately 40% for around 1 month (day 27–day 55) without the use of alkaline reagents but did not increase during further operation. Quantitative elemental analysis revealed Mn oxides on the sand filters during the Mn removal period. The bacterial communities on the RSFs, recorded on day 42 and day 85, were characterized and compared using 16S rRNA gene amplicon sequencing. Although the well-known Mn-oxidizing bacteria (MOB) were not listed among the ten most dominant operational taxonomic units (OTUs) on the sand filters (relative abundances: >0.68%), a significant increase in the OTUs related to well-known alphaproteobacterial MOB, such as Pedomicrobium spp., were observed during the period.

Microbial Community Responses to Alterations in Historical Fire Regimes in Montane Grasslands

The influence of fire regimes on soil microbial diversity in montane grasslands is a relatively unexplored area of interest. Understanding the belowground diversity is a crucial stepping-stone toward unravelling community dynamics, nutrient sequestration, and overall ecosystem stability. In this study, metabarcoding was used to unravel the impact of fire disturbance regimes on bacterial and arbuscular mycorrhizal fungal community structures in South African montane grasslands that have been subjected to an intermediate (up to five years) term experimental fire-return interval gradient. Bacterial communities in this study exhibited a shift in composition in soils subjected to annual and biennial fires compared to the controls, with carbon and nitrogen identified as significant potential chemical drivers of bacterial communities. Shifts in relative abundances of dominant fungal operational taxonomic units were noted, with Glomeromycota as the dominant arbuscular mycorrhiza observed across the fire-return gradient. A reduction in mycorrhizal root colonisation was also observed in frequently burnt autumnal grassland plots in this study. Furthermore, evidence of significant mutualistic interactions between bacteria and fungi that may act as drivers of the observed community structure were detected. Through this pilot study, we can show that fire regime strongly impacts bacterial and fungal communities in southern African montane grasslands, and that changes to their usually resilient structure are mediated by seasonal burn patterns, chemical drivers, and mutualistic interactions between these two groups.

Bacteria are more sensitive than fungi to soil fertility in an intensive vegetable field

Partial substitution of chemical nitrogen (N) fertilizers with organic amendments is important for improving soil fertility and crop yield. Microorganisms play an important role in soil fertility by driving energy and nutrient cycles in the soil. However, there is limited information on the link between soil fertility and the microbial community under organic substitutions. Here, we investigated the soil fertility index and fertilization-sensitive operational taxonomic units (OTUs) of bacterial and fungal communities under different organic N substitution rates from 0 % to 100 % during four years of constant fertilization in an intensively-farmed vegetable field. Our results demonstrated that the 20 % and 50 % substitution rates could improve the soil fertility by 35.0 % and 27.5 %, respectively, compared with the 0 % substitution rate while ensuring crop yield. The 20 % to 100 % substitution rates significantly increased bacterial richness and diversity, as well as fungal diversity, compared with the 0 % substitution rate. Bacterial communities showed many more differences between the 0 % and other organic substitutions than in the fungal communities. Of the bacterial networks, the dominant sensitive OTUs are Phycisphaerae and Acidobacteria Subgroup_6 for the 0 % substitution rate and Gammaproteobacteria and Alphaproteobacteria for other organic substitutions. Of the fungal networks, Sordariomycetes and Pezizomycetes were the dominant sensitive OTUs in all fertilization treatments. The assembly patterns of bacterial and fungal communities were induced toward deterministic processes under chemical N fertilization, which were restrained from this process under organic N fertilization. Furthermore, soil fertility produced a significant influence on the bacterial community (dominated by deterministic processes) but not on the fungal community (dominated by stochastic processes). In conclusion, understanding the survival patterns of fertilization-sensitive microorganisms is fundamental to manage soil fertility, which will help to address the needs of targeted smart agriculture through the cultivation of specific microbial taxa in the future.

Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation.

Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community.

Application of DNA Metabarcoding for Identifying the Diet of Asian Clam (Corbicula fluminea, Müller, 1774)

Corbicula has often been reported as one of the most invasive freshwater species in the world. It plays an important role in the food chains of brackish water zones in Korea, where it is predominant. However, detailed information on the Corbicula diet is still lacking. The purpose of this study was to identify the potential prey of Corbicula fluminea in the Seomjin River using a DNA metabarcoding approach, as very little is known about its feeding selectivity in natural conditions. A survey was conducted at two study sites (1 and 2) in the Seomjin River in November 2021. The two sites were selected based on increasing salinity gradient. The dominant operational taxonomic unit in the pseudofeces and gut content of C. fluminea was Microcyclops varicans (Copepoda) and Oncorhynchus mykiss (Fish), respectively. The alpha diversity at site 1 was higher than that at site 2. More diverse potential prey species were identified at the site with low salinity (i.e., site 1). The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex estuarine ecosystem.

Effects of Dam Building on Niche Differentiation of Comammox Nitrospira in the Main Stream of the Three Gorges Reservoir Area

Complete ammonia oxidizers (comammox) can completely oxidize ammonia to nitrate, and the various habitats of comammox Nitrospira are an important guarantee for their survival. The construction of the Three Gorges Dam, China, made it easier for nitrogen to stay in the reservoir area, which may have caused the niche differentiation of comammox, thereby affecting the natural transformation process of nitrogen in the reservoir area. This study investigated comammox in river sediments in the Three Gorges Reservoir area. Comammox clade A and comammox clade B were detected in all samples, and comammox clade A was dominant. The number of dominant OTUs (Operational Taxonomic Unit) in comammox clade A.1 accounted for 18.69% of the total number of OTUs, followed by comammox clade A.2 (18.58%) and clade B (14.30%). The indicated abundance of comammox Nitrospira clade A and clade B amoA genes in the main stream of the Three Gorges Reservoir increased along the length of the river and reached the maximum in the middle part of the reservoir area. The highest abundance of ammonia-oxidizing archaea (AOA) amoA genes appeared in the upper stream section of the reservoir area. Comammox Nitrospira clade A exhibited the highest abundance (3.00 × 104 ± 8782.37 copies/g), followed by comammox Nitrospira clade B (1.83 × 103 ± 1019.82 copies/g), ammonia-oxidizing bacteria (AOB) (1.28 × 103 ± 574.69 copies/g), and AOA (1.73 × 102 ± 48.05 copies/g). The abundances of both comammox clades A and B were positively correlated with sediment pH, indicating that pH is an important environmental factor affecting the growth of comammox bacteria. Additionally, the relative abundances of both comammox clade A.2 and clade B were significantly correlated with overlying water dissolved oxygen (DO) in the reservoir area. This study thus indicated that there exists a niche differentiation of comammox Nitrospira in the main stream of the Three Gorges Reservoir area. The potential changes in the ammoxidation process and the environmental effects caused by this niche differentiation need further attention.

Effects of environmental factors on low temperature anaerobic digestion of pig manure

In this study, we investigated the inhibitory effect of low temperature on biogas fermentation system. Biogas fermentation inoculum was domesticated at 4 °C, and subsequently inoculated into pig manure feedstock in a batch biogas fermentation process. A low-temperature biogas fermentation system was maintained at 9 °C, and its abiotic factors, bacterial community, and archaeal community were determined. The results showed that (1) the biogas fermentation lasted for 160 days, with a total gas production of 19,150 ml, including N2 production of 11,370 ml, CO2 production of 3,534 ml, and CH4 production of 3,031 ml. (2) The average relative abundance of the primary dominant bacterium operational taxonomic unit (OTU) was 30%, with 100% similarity to Pseudomonas caeni , atypical denitrifying bacterium. The average relative abundance of the secondary dominant bacterium OTU was 20.36%, with 99% similarity to Clostridium cellulovorans, a typical cellulose- and hemicellulose-degrading bacterium. The average relative abundance of the primary dominant methanogenic archaeon OTU was 7.22%, with 99% similarity to Methanosphaera cuniculi, a typical methylotrophic methanogen, and the secondary dominant methanogenic archaeon OTU had an average relative abundance of 4.15%, with 98% similarity to Methanocorpusculum sinense, a typical hydrogenotrophic methanogen. (3) The primary dominant bacterial genus Pseudomonas exhibited highly significant negative correlations with the dominant biogas-producing microorganisms such as Clostridium, Terrisporobacter, Turicibacter, Methanosphaera, and Methanocorpusculum. We concluded that (1) high concentrations of abiotic factors such as ammonia nitrogen, acetic acid, and propionic acid were important indicators of relatively poor operation of low-temperature biogas fermentation systems, while (2) high numbers of MCG archaea and Pseudomonas were important biotic factors showing comparatively poor operation of the system.

Differential oral microbiome in nonhuman primates from periodontitis-susceptible and periodontitis-resistant matrilines.

Rhesus monkeys (n=36) exhibiting a healthy periodontium at baseline were used to induce progressing periodontitis through ligature placement around premolar/molar teeth. Bacterial samples were collected at baseline, 0.5, 1, and 3 months of disease and at 5 months for disease resolution. The animals were distributed into two groups (18/group): 3-7 years (young) and 12-23 years (adult) and stratified based upon matriline susceptibility to periodontitis (PDS, susceptible; PDR, resistant). A total of 444 operational taxonomic units (OTUs) with 100 microbes representing a core microbiome present in ≥75% of the samples were identified. Only 48% of the major phylotypes overlapped in the PDS and PDR samples. Different OTU abundance patterns were seen in young animals from the PDS and PDR matrilines, with qualitative similarities during disease and the relative abundance of phylotypes becoming less diverse. In adults, 23 OTUs were increased during disease in PDS samples and 24 in PDR samples; however, only five were common between these groups. Greater diversity of OTU relative abundance at baseline was observed with adult compared to young oral samples from both the PDS and PDR groups. With disease initiation (2weeks), less diversity of relative abundance and some distinctive increases in specific OTUs were noted. By 1 month, there was considerable qualitative homogeneity in the major OTUs in both groups; however, by 3 months, there was an exacerbation of both qualitative and quantitative differences in the dominant OTUs between the PDS and PDR samples. These results support that some differences in disease expression related to matriline (familial) periodontitis risk may be explained by microbiome features.

Evaluation of four primer sets for analysis of comammox communities in black soils.

Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox amoA genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Nitrospira Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO3–-N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.

Response of Soil Fertility and Bacterial Community Composition to Vegetation Species in a Coal Mining Subsidence Area: A Survey After 20-Year Reclamation

Revegetation is an important restoration approach after reclamation in coal mining subsidence area. However, few studies have paid attention to the impacts of different vegetation species on soil fertility and bacterial community composition in the reclamation area filled with fly ash for a long time. In this study, soil fertility and bacterial community composition were investigated in a non-subsidence area (FCK) and a coal mining subsidence reclamation area restored vegetation with woody plants (pagoda trees, FS; peach trees, FP) and herbaceous plants (wheat-maize rotation, FW) for 20 years. Results showed that topsoil and subsoil nutrients including available K and alkali-hydrolyzable N, soil organic matter, and total carbon in the non-subsidence site were significantly higher than those in reclamation sites. Topsoil fertility indices (SFI) in reclamation sites were lower than that in non-subsidence site, and soil fertility index in FW was higher than that in FS and FP. Moreover, the SFI in topsoil (from −0.24 to 2.08) was significantly higher than that in subsoil (from −1.12 to −0.39). 16S rRNA gene sequencing analysis showed Proteobacteria, Acidobacteria and Actinobacteria were the dominant bacterial phyla in all sites, but the subsoil bacterial alpha indices (Shannon and Simpson) in the non-subsidence site were higher than those in reclamation sites. Principal coordinates analysis and non-metric multidimensional scaling analysis showed that the bacterial community composition in reclamation sites was significantly different from that in the non-subsidence site, and they were similar in the soil with wheat-maize rotation model between non-subsidence and reclamation sites. Co-occurrence network analysis noted that the network of dominant bacterial operational taxonomic units in the subsoil was more complex than that in the topsoil. Redundancy analysis suggested soil pH in topsoil and subsoil was an important driving factor for soil bacteria community composition. Overall, the reclamation site with the wheat-maize rotation model had higher soil fertility and bacterial community composition was similar to that of the non-subsidence site, indicating revegetation with the wheat-maize rotation model is a good reclamation approach to improve soil fertility in coal mining subsidence area.

DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing.

Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population-level studies.

Investigation of soil microbiota reveals variable dominant species at different land areas in China

Soil microbiota is associated with plant growth and nutrition. Investigation of plant–soil interaction is essential for revealing the changes of microbial dynamics in the soil. Vegetation types and human activities, such as agriculture, had severely affected soil microbial structure and function. In this study, 16S rRNA were analysed to identify microbial structures in the soil. The total organic carbon (TOC) and total nitrogen (TN) in these soil samples were also analysed. TOC and TN in these soil samples were different, which might be due to different vegetation types. The main phyla in these soil samples were Actinobacteria, Proteobacteria and Acidobacteria. Furthermore, the genera in these soil groups were highly diverse, and most of the bacteria could not be assigned to any known genus. This indicated the presence of novel bacterial genera in these soil samples. A fraction of the dominant operational taxonomic units in the soil microbiota was identified, several of which played functional roles in soil nutrition. The linkage between the soil microbiota, especially the dominant species, and soil nutrients was analysed in this study. The culturomics and other omics technologies would help to isolate some novel microorganisms, which might lead to the recovery of functional microbial agents for plant growth.

Dominance of arbuscular mycorrhizal fungi is key for Mongolian steppe management under livestock grazing, as indicated by ecosystem multifunctionality

Livestock grazing of drylands supports millions of livelihoods worldwide; however, overgrazing causes severe biodiversity loss and degrades ecosystem functions. Understanding the effects of grazing intensity, aridity, and soil microbes is required for sustainable management. Here, we focused on arbuscular mycorrhizal (AM) fungi in soils and roots and examined their relationship with ecosystem multifunctionality under livestock grazing of Mongolian grasslands with different aridity levels. Above- and below-ground plant biomass were used to measure ecosystem-service multifunctionality, excluding annual plants that are unfavorable for ecosystem function and rangeland management. In both mountain forest steppe (mean annual precipitation = 207.7 mm) and steppe–desert steppe transition zone (mean annual precipitation = 128.4 mm), ecosystem multifunctionality was decreased by livestock grazing, as indicated by palatable plant shoot biomass. In line with the multifunctionality, the dominant plant species, Stipa krylovii, and AM plant biomass were decreased by livestock grazing. The Berger–Parker dominance index of soil AM fungi and Simpson’s diversity had a positive and negative relationship with multifunctionality, respectively, indicating that dominant AM fungi rather than AM fungal diversity in soil are key for maintaining multifunctionality. Root and soil AM fungal communities were significantly different with dominance of Rhizophagus operational taxonomic units (OTUs) in roots and Claroideoglomus OTUs in soil. However, the similarity between soil and root AM fungal communities increased with livestock grazing. Correlation analysis between palatable plant biomass and relative abundance of dominant AM fungal OTUs identified indicator virtual taxa that decreased (VTX00325 in roots, and VTX00165, VTX00214, and VTX00222 in soil) or increased (VTX00100, VTX00130, and VTX00295 in soil) with grazing intensity. The OTUs that were increased by grazing may be r-selected, grazing-tolerant AM fungi that accept a low C supply and supply few nutrients to plants. Our results suggest that grassland management focusing on ecosystem-service multifunctionality via control of AM plants, including S. krylovii and their co-dominant dominant AM fungi, in ungrazed grasslands are key for sustainable rangeland management in Mongolia.