Seasonal Change of Sediment Microbial Communities and Methane Emission in Young and Old Mangrove Forests in Xuan Thuy National Park

Microbial communities in mangrove forests have recently been intensively investigated to explain the ecosystem function of mangroves. In this study, the soil microbial communities under young (<11 years-old) and old (>17 years-old) mangroves have been studied during dry and wet seasons. In addition, biogeochemical properties of sediments and methane emission from the two different mangrove ages were measured. The results showed that young and old mangrove soil microbial communities were significantly different on both seasons. Seasons seem to affect microbial communities more than the mangrove age does. Proteobacteria and Chloroflexi were two top abundant phyla showing >15%. Physio-chemical properties of sediment samples showed no significant difference between mangrove ages, seasons, nor depth levels, except for TOC showing significant difference between the two seasons. The methane emission rates from the mangroves varied depending on seasons and ages of the mangrove. However, this did not show significant correlation with the microbial community shifts, suggesting that abundance of methanogens was not the driving factor for mangrove soil microbial communities.

Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.

The complete mitochondrial genome of a marine polychaete, Prionospio cf. japonica (Annelida: Spionidae)

Prionospio Malmgren 1867 is one of the abundant genera of the family Spionidae Grube, 1850. Despite its rich diversity, information on their complete mitochondrial genome has remained unknown. In this study, we determined the complete mitochondrial genome of a spionid polychaete, Prionospio cf. japonica Okuda 1935. The specimen was collected from the fine sand in the intertidal zone of South Korea. The mitogenome consists of 15,267 base pairs, harboring 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The maximum-likelihood phylogenetic tree based on the 11 PCGs showed that Prionospio cf. japonica grouped with other spionid polychaetes and formed a monophyletic group. Also, the mtDNA of P. cf. japonica was more closely related to that of non-polydorin spionid, Marenzelleria neglecta, than polydorin spionids. The molecular data will be valuable for studying evolutionary relationships among annelids.

Domestication shapes the endophytic microbiome and metabolome of Salicornia europaea

AIMS

We aim at understanding the effect of domestication on the endophytic microbiome and metabolome of Salicornia europaea and collecting evidence on the potential role of microbial populations and metabolites in the adaptation of plants to different ecological contexts (wild vs crops).

METHODS AND RESULTS

Samples were collected from a natural salt marsh (wild) and an intensive crop field (crop). High-throughput sequencing of the 16S rRNA gene, gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) were used to analyze the endophytic bacterial communities and the metabolite profiles of S. europaea roots, respectively. The elemental analysis of the plant shoots was performed by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS).Overall, significant differences were found between the microbiome of wild and cultivated plants. The later showed a higher relative abundance of the genera Erythrobacter, Rhodomicrobium, and Ilumatobacter than wild plants. The microbiome of wild plants was enriched in Marinobacter, Marixanthomonas, and Thalassospira. The metabolite profile of crop plants revealed higher amounts of saturated and non-saturated fatty acids and acylglycerols. In contrast, wild plants contained comparatively more carbohydrates and most macroelements (i.e. Na, K, Mg, and Ca).

CONCLUSIONS

There is a strong correlation between plant metabolites and the endosphere microbiome of S. europaea. In wild populations, plants were enriched in carbohydrates and the associated bacterial community was enriched in genes related to primary metabolic pathways such as nitrogen metabolism and carbon fixation. The endosphere microbiome of crop plants was predicted to have higher gene counts related to pathogenesis. Crop plants also exhibited higher amounts of azelaic acid, an indicator of exposure to phytopathogens.

Root exudates and rhizosphere microbiomes jointly determine temporal shifts in plant-soil feedbacks

Plants influence numerous soil biotic factors that can alter the performance of later growing plants-defined as plant-soil feedback (PSF). Here, we investigate whether PSF effects are linked with the temporal changes in root exudate diversity and the rhizosphere microbiome of two common grassland species (Holcus lanatus and Jacobaea vulgaris). Both plant species were grown separately establishing conspecific and heterospecific soils. In the feedback phase, we determined plant biomass, measured root exudate composition, and characterised rhizosphere microbial communities weekly (eight time points). Over time, we found a strong negative conspecific PSF on J. vulgaris in its early growth phase which changed into a neutral PSF, whereas H. lanatus exhibited a more persistent negative PSF. Root exudate diversity increased considerably over time for both plant species. Rhizosphere microbial communities were distinct in conspecific and heterospecific soils and showed strong temporal patterns. Bacterial communities converged over time. Using path models, PSF effects could be linked to the temporal dynamics of root exudate diversity, whereby shifts in rhizosphere microbial diversity contributed to temporal variation in PSF to a lesser extent. Our results highlight the importance of root exudates and rhizosphere microbial communities in driving temporal changes in the strength of PSF effects.

Penoxsulam-resistant barnyardgrass-mediated rhizosphere microbial communities affect the growth of rice

BACKGROUND

The incidence of herbicide-resistant barnyardgrass is escalating in paddy fields, yet the interactions between resistant weeds and rice are largely unknown. The microbiota of herbicide-resistant barnyardgrass rhizosphere soil is critical for both barnyardgrass and rice fitness.

RESULTS

Rice has different biomass allocation and root traits in the presence of penoxsulam-resistant versus penoxsulam-susceptible barnyardgrass or in their conditioned soil. Compared to susceptible barnyardgrass, resistant barnyardgrass led to an allelopathic increase in rice root, shoot, and whole-plant biomasses. Resistant barnyardgrass recruited distinct core and unique microbes in rhizosphere soil compared to susceptible barnyardgrass. In particular, resistant barnyardgrass assembled more Proteobacteria and Ascomycota to enhance plant stress tolerance. Furthermore, the root exudates from resistant and susceptible barnyardgrass were responsible for the assembly and establishment of the root microbial structure. Importantly, (-)-loliolide and jasmonic acid in root exudates were correlated with the core microbes in the rhizosphere soil.

CONCLUSION

The interference of barnyardgrass with rice can be mediated by rhizosphere microbial communities. Biotype-specific variation in the ability to generate soil microbial communities appears to ameliorate the negative consequences for rice growth, providing an intriguing possibility for modulation of the rhizosphere microbiota to increase crop productivity and sustainability. © 2023 Society of Chemical Industry.

Epidemiological and Molecular Characteristics of bla NDM-1 and bla KPC-2 Co-Occurrence Carbapenem-Resistant Klebsiella pneumoniae

Objective

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged and spread worldwide. It can usually cause a serious threat complicating treatment options in clinical settings. However, treatment options are limited. The present study investigates the prevalence and genetic characteristics of bla _NDM-1 and bla _KPC-2 co-harboring clinical isolates of Klebsiella pneumoniae.

Methods

In this study, Multiplex polymerase chain reaction (PCR) was performed to detect the carbapenem-resistant genes, and the broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) of antibacterial drugs. The transferability of carbapenem-resistant phenotypes was examined using filter mating assays. Overall, we used Illumina sequencing to evaluate the epidemiological and molecular characteristics of bla _NDM-1 and bla _KPC-2 (genes encoding carbapenemase) co-occurrence in CRKP strains.

Results

All strains exhibited resistance to carbapenems and other antibiotics. However, they were still susceptible to polymyxin E. Among them, 18 isolates were positive for bla _KPC-2, bla _NDM-1, and multiple virulence determinants, such as genes encoding the virulence factor aerobactin, yersiniabactin, and the regulator of the mucoid phenotype (rmpA and rmpA2). Whole genome sequencing revealed that the 18 CRKP strains belonged to ST11 and capsular serotype KL64, and could be grouped into two evolutionary branches. Furthermore, these strains displayed hypervirulence potential since all of them carried pLVPK-like plasmid.

Conclusion

These findings suggested that ST11-KL64 CRKP strains are major threats in terms of nosocomial infections in this hospital. Hence, new strategies should be urgently developed to monitor, diagnose, and treat this high-risk CRKP clone.

Short-Term Vegetation Restoration Enhances the Complexity of Soil Fungal Network and Decreased the Complexity of Bacterial Network

Different vegetation restoration methods may affect the soil’s physicochemical properties and microbial communities. However, it is not known how the microbial network’s complexity of the bacterial and fungal communities respond to short-term vegetation restoration. We conducted a short-term ecological restoration experiment to reveal the response of the soil’s microbial community and microbial network’s stability to initial vegetation restoration during the restoration of the degraded grassland ecosystem. The two restoration methods (sowing alfalfa (Medicago sativa, AF) and smooth brome (Bromus inermis, SB)) had no significant effect on the alpha diversity of the fungal community, but the SB significantly increased the alpha diversity of the soil surface bacterial community (p < 0.01). The results of NMDS showed that the soil’s fungal and bacterial communities were altered by a short-term vegetation restoration, and they showed that the available phosphorus (AP), available potassium (AK), and nitrate nitrogen (nitrate-N) were closely related to changes in bacterial and fungal communities. Moreover, a short-term vegetation restoration significantly increased the complexity and stability of fungi ecological networks, but the opposite was the case with the bacteria. Our findings confirm that ecological restoration by sowing may be favorable to the amelioration of soil fungi complexity and stability in the short-term. Such findings may have important implications for soil microbial processes in vegetation recovery.

The Roles of TP53 and FGFR2 in Progress Made Treating Endometrial Cancer

The morbidity and mortality caused by endometrial cancer (EC) is still rising worldwide. In recent years, a new system of tumor stratification has been proposed based on POLE-mutational status, TP53, and microsatellite stability status. The aim of the study was to analyze a vast panel on the genes potentially involved in the genesis of endometrial cancer in the Polish population. One hundred and three white female patients with confirmed endometrial cancer were enrolled on the study. We performed sequencing using the Hot Spot Illumina panel and microsatellite stability with immunohistochemistry. We confirmed a key role of the TP53 mutation in progress to high-grade EC and parallelly some role of FGFR2 mutation. Moreover, our data present a vast landscape of mutations in EC and their polymorphism. We reported the meaning of FGFR2 mutation and TP53 (high copy number) in high-grade ECs. Our observation in MSI contribution is comparable with other studies. Finally, we see a strong need for the implementation of the TCGA classification.

Polar Cryoconite Associated Microbiota Is Dominated by Hemispheric Specialist Genera

Cryoconite holes, supraglacial depressions containing water and microbe-mineral aggregates, are known to be hotspots of microbial diversity on glacial surfaces. Cryoconite holes form in a variety of locations and conditions, which impacts both their structure and the community that inhabits them. Using high-throughput 16S and 18S rRNA gene sequencing, we have investigated the communities of a wide range of cryoconite holes from 15 locations across the Arctic and Antarctic. Around 24 bacterial and 11 eukaryotic first-rank phyla were observed in total. The various biotic niches (grazer, predator, photoautotroph, and chemotroph), are filled in every location. Significantly, there is a clear divide between the bacterial and microalgal communities of the Arctic and that of the Antarctic. We were able to determine the groups contributing to this difference and the family and genus level. Both polar regions contain a "core group" of bacteria that are present in the majority of cryoconite holes and each contribute >1% of total amplicon sequence variant (ASV) abundance. Whilst both groups contain Microbacteriaceae, the remaining members are specific to the core group of each polar region. Additionally, the microalgal communities of Arctic cryoconite holes are dominated by Chlamydomonas whereas the Antarctic cryoconite holes are dominated by Pleurastrum. Therefore cryoconite holes may be a global feature of glacier landscapes, but they are inhabited by regionally distinct microbial communities. Our results are consistent with the notion that cryoconite microbiomes are adapted to differing conditions within the cryosphere.

Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation

Soil washing and landfarming processes are widely used to remediate total petroleum hydrocarbon (TPH)-contaminated soil, but the impact of these processes on soil bacteria is not well understood. Four different states of soil (uncontaminated soil (control), TPH-contaminated soil (CS), after soil washing (SW), and landfarming (LF)) were collected from a soil remediation facility to investigate the impact of TPH and soil remediation processes on soil bacterial populations by metagenomic analysis. Results showed that TPH contamination reduced the operational taxonomic unit (OTU) number and alpha diversity of soil bacteria. Compared to SW and LF remediation techniques, LF increased more bacterial richness and diversity than SW, indicating that LF is a more effective technique for TPH remediation in terms of microbial recovery. Among different bacterial species, Proteobacteria were the most abundant in all soil groups followed by Actinobacteria, Acidobacteria, and Firmicutes. For each soil group, the distribution pattern of the Proteobacteria class was different. The most abundant classed were Alphaproteobacteria (16.56%) in uncontaminated soils, Deltaproteobacteria (34%) in TPH-contaminated soils, Betaproteobacteria (24%) in soil washing, and Gammaproteobacteria (24%) in landfarming, respectively. TPH-degrading bacteria were detected from soil washing (23%) and TPH-contaminated soils (21%) and decreased to 12% in landfarming soil. These results suggest that soil pollution can change the diversity of microbial groups and different remediation techniques have varied effective ranges for recovering bacterial communities and diversity. In conclusion, the landfarming process of TPH remediation is more advantageous than soil washing from the perspective of bacterial ecology.

Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA

Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5'-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.

Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units

Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units of a hospital in Brazil. While our results demonstrate that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.

The complete chloroplast genome sequence of Rotheca myricoides (Hochst.) Steane & Mabb., a traditional medicinal plant

Rotheca myricoides (Hochst.) Steane & Mabb. is a plant species used in traditional medicine for the management of diabetes in the lower eastern part of Kenya (Kitui, Machakos and Makueni Counties, Kenya) that is mainly inhabited by the Kamba community. The complete chloroplast genome sequence of R. myricoides was assembled from the whole genome Illumina sequencing data. The genome was 150,596 bp in length, contained an SSC region of 17,237 bp and LSC region of 83,489 bp, separated by IRs of 24,935 bp, each. The genome contained 114 unique genes, including 80 PCGs, 4 rRNA genes, and 30 tRNA genes. In addition, 18 genes contained one or two introns, including 10 PCG genes with a single intron, 2 PCG genes harboring two introns, and 6 tRNA genes harboring a single intron. Phylogenetic analysis supported R. myricoides had the closest genetic relationship with Rotheca serrata and clustered with the Rotheca family species.

Transcriptome Profiling Reveals a Divergent Adaptive Response to Hyper- and Hypo-Salinity in the Yellow Drum, Nibea albiflora

Simple Summary

Global warming and certain climate disasters (typhoon, tsunami, etc.) can lead to fluctuation in seawater salinity that causes salinity stress in fish. The aim of this study was to investigate the functional genes and relevant pathways in response to salinity stress in the yellow drum. Genes and pathways related to signal transduction, osmoregulation, and metabolism may be involved in the adaptive regulation to salinity in the yellow drum. Additionally, the genes under salinity stress were mainly divided into three expression trends. Our results provided novel insights into further study of the salinity adaptability of euryhaline fishes.

Abstract

The yellow drum (Nibea albiflora) is an important marine economic fish that is widely distributed in the coastal waters of the Northwest Pacific. In order to understand the molecular regulatory mechanism of the yellow drum under salinity stress, in the present study, transcriptome analysis was performed under gradients with six salinities (10, 15, 20, 25, 30, and 35 psu). Compared to 25 psu, 907, 1109, 1309, 18, and 243 differentially expressed genes (DEGs) were obtained under 10, 15, 20, 30, and 35 psu salinities, respectively. The differential gene expression was further validated by quantitative real-time PCR (qPCR). The results of the tendency analysis showed that all DEGs of the yellow drum under salinity fluctuation were mainly divided into three expression trends. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the PI3K-Akt signaling pathway, Jak-STAT signaling pathway as well as the glutathione metabolism and steroid biosynthesis pathways may be the key pathways for the salinity adaptive regulation mechanism of the yellow drum. G protein-coupled receptors (GPCRs), the solute carrier family (SLC), the transient receptor potential cation channel subfamily V member 6 (TRPV6), isocitrate dehydrogenase (IDH1), and fructose-bisphosphate aldolase C-B (ALDOCB) may be the key genes in the response of the yellow drum to salinity stress. This study explored the transcriptional patterns of the yellow drum under salinity stress and provided fundamental information for the study of salinity adaptability in this species.

The complete chloroplast genome sequence of Camellia rostrata S. X. Yang & S. F. Chai (Theaceae), a critically endangered yellow camellia from southwest China

Camellia rostrata S. X. Yang & S. F. Chai is a recently described yellow camellia species from Guangxi, China. It is a critically endangered species according to the IUCN Red List Categories and Criteria. Here, we report the complete chloroplast (cp) genome based on next-generation sequencing technology. The complete cp genome of C. rostrata is 156,547 bp in length and consists of a large single-copy (LSC, 86,199 bp) region, a small single-copy (SSC, 18,204 bp) region, and a pair of inverted repeats (IRs, 26,072 bp). The genome contains 135 genes including 40 tRNA, eight rRNA, and 87 protein-coding genes. Phylogenetic analysis resolved C. rostrata in a clade containing C. huana and C. impressinervis, both of which are classified to Camellia sect. Archecamellia. Our findings support the placement of C. rostrata in C. sect. Archecamellia as proposed by a previous study. The cp genome of C. rostrata provides valuable bioinformatic resources for the protection and utilization of this yellow camellia species.

High level of conservation and diversity among the endophytic seed bacteriome in eight alpine grassland species growing at the Qinghai Tibetan Plateau

Seed borne microorganisms play an important role in plant biology. Concerns have recently been raised about loss of seed microbial diversity by seed treatments, crop domestication and plant breeding. Information on the seed microbiomes of native plants growing in natural ecosystems is beneficial as they provide the best settings to detect indigenous plant microbe interactions. Here, we characterized the seed bacterial community of 8 native alpine grassland plants. First, seed bacterial diversity was examined using Illumina DNA sequencing, then 28 cultivable bacteria were isolated and potential functions were explored. Across 8 plant species, 343 different bacterial genera were identified as seed endophytes, 31 of those were found in all plant species, indicating a high level of conservation. Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the top five dominant phyla. Plant species identity was a key determinant shaping the seed endophytic bacteriome. ACC deaminase activity, siderophores production and secretion of lytic enzymes were common functions shown by isolated bacteria. Our results demonstrate that highly diverse and beneficial bacterial populations are hosted by seeds of alpine grassland species to ensure the establishment of best bacterial symbionts for the next generation. This information is useful for crop improvement by reinstating beneficial seed microbial diversities for high-quality forage and crop seeds.

Fungal Community Composition and Diversity Vary With Soil Horizons in a Subtropical Forest

Soil fungal communities, which drive many ecosystem processes, vary across soil horizons. However, how fungal communities are influenced by soil horizon layers remains largely unstudied. In this study, soil samples were collected from the organic horizon (O horizon) and mineral matter horizon (M horizon) in two sites of Dabie Mountain, China, and the effects of the two horizons on the soil fungal community composition were assessed based on Illumina MiSeq sequencing. Our results showed that soil fungal community composition varied with soil horizons, and soil fungal species richness and diversity in the O horizon were significantly higher than that in the M horizon. Total organic carbon (TOC), total organic nitrogen (TON), alkali-hydrolyzable nitrogen (AHN), available potassium (AK), and available phosphorus (AP) significantly influenced fungal community composition, abundance, and diversity across the two horizons (P < 0.05). Furthermore, precipitation was found to have a significant effect on fungal community composition. Our results demonstrate changes in fungal communities across soil horizons and highlight the importance of soil organic matter on fungal communities and diversity.

Effects of Lactobacillus rhamnosus and Enterococcus faecalis Supplementation as Direct-Fed Microbials on Rumen Microbiota of Boer and Speckled Goat Breeds

The effects on rumen microbial communities of direct-fed probiotics, Lactobacillus rhamnosus and Enterococcus faecalis, singly and in combination as feed supplements to both the Boer and Speckled goats were studied using the Illumina Miseq platform targeting the V3-V4 region of the 16S rRNA microbial genes from sampled rumen fluid. Thirty-six goats of both the Boer and Speckled were divided into five experimental groups: (T1) = diet + Lactobacillus rhamnosus; (T2) = diet + Enterococcus faecalis; (T3) = diet + Lactobacillus rhamnosus + Enterococcus faecalis; (T4, positive control) = diet + antibiotic and (T5, negative control) = diet without antibiotics and without probiotics. Our results revealed that Bacteroidetes, Firmicutes, TM7, Proteobacteria, and Euryarchaeota dominate the bacterial communities. In our observations, Lactobacillus rhamnosus and Enterococcus faecalis supplements reduced the archaeal population of Methanomassiliicocca in the T1, T2 and T3 groups, and caused an increase in the T4 group. Chlamydiae were present only in the T5 group, suggesting that probiotic and antibiotic inhibit the growth of pathogens in the rumen. We inferred, based on our results, that Lactobacillus rhamnosus and Enterococcus faecalis favour the survival of beneficial microbial communities in the goats’ rumen. This may lead to an overall improved feed efficacy and growth rate.

Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo's fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

Allium cepa L. Inoculation with a Consortium of Plant Growth-Promoting Bacteria: Effects on Plants, Soil, and the Autochthonous Microbial Community

The present work was aimed at investigating the effects of a four bacterial strain consortium—Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Burkholderia ambifaria—on Allium cepa L. and on soil health. The bacterial consortium was inoculated on seeds of two different onion varieties; inoculated and Control seeds (treated with autoclaved inoculum) were sown in an open-field and followed until harvest. Plant growth development parameters, as well as soil physico–chemical and molecular profiles (DNA extraction and 16S community sequencing on the Mi-Seq Illumina platform), were investigated. The results showed a positive influence of bacterial application on plant growth, with increased plant height (+18%), total chlorophylls (+42%), crop yields (+13%), and bulb dry matter (+3%) with respect to the Control. The differences between Control and treatments were also underlined in the bulb extracts in terms of total phenolic contents (+25%) and antioxidant activities (+20%). Soil fertility and microbial community structure and diversity were also positively affected by the bacterial inoculum. At harvest, the soil with the presence of the bacterial consortium showed an increase in total organic carbon, organic matter, and available phosphorus, as well as higher concentrations of nutrients than the Control. The ecological indexes calculated from the molecular profiles showed that community diversity was positively affected by the bacterial treatment. The present work showed the effective use of plant growth-promoting bacteria as a valid fertilization strategy to improve yield in productive landscapes whilst safeguarding soil biodiversity.

Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery

In order to effectively use microbial-based strategies to manage anaerobic digesters, it is necessary to distinguish between community shifts that are part of the natural dynamic of the system and shifts caused by environmental or operational disturbances. The objective of this research study was to evaluate the significance of changes in the microbial community of anaerobic digesters during failure in correlation to operational parameters such as an organic acid overload. Five continuously stirred 0.5 L reactors were set-up as semi-continuously-fed, mesophilic dairy manure digesters with a 30-day hydraulic retention time. After a 120-day stabilization period, two digesters were kept as controls, while the organic loading rates in the triplicate set were increased step-wise to ultimately provide a shock-load leading to failure using propionic acid spikes. Acidosis resulting in near cessation of biogas and termination of methane production occurred between 4 and 7 weeks, after which all the digesters continued to be fed only dairy manure. The shock loading of propionic acid led to an accumulation of mainly acetate and propionate, with low levels of iso-butyrate, butyrate, iso-valerate, and valerate. High-throughput Illumina sequencing of the V4 region of the bacterial and archaeal 16S rRNA gene in digester samples showed a significant change in the microbial community composition during propionic acid overload, followed by a return to the original composition with regular feedstock. Bacterial genera whose relative abundance decreased during the inhibition stage included Sedimentibacter, Syntrophomonas, TSCOR003.O20, and Marinilabiaceae, while the relative abundance of Lachnospiraceae, Ruminococcus, Mogibacteriaceae, Pyramidobacter, and Bacteroides increased. The relative abundance of dominant methanogens, Methanosarcina and Methanobacterium, although initially resistant, were decreased (from 91.71 to 12.14% and from 2.98 to 0.73%, respectively) during inhibition, while Methanobrevibacter and Methanosphaera that were prominent in the manure feedstock increased from 17.36 to 79.45% and from 0.14 to 1.12%, respectively. Shifts in bacterial and archaeal compositions, back to their pre-shock steady state after failure, highlight the digester's microbial resilience and recovery potential.

Effect of Different Grain for Green Approaches on Soil Bacterial Community in a Karst Region

Soil bacteria participate in nutrient cycling above and below ground to promote ecosystem stability and health. However, the relationship of soil bacteria and environmental factors following the Grain for Green (GfG) program remains poorly understood in southwest China. Soil samples were collected from seven Grain for Green sites that had been revegetated for 15 years. Four of these sites were afforested with a different tree species: Zenia insignis (ZI), Toona sinensis (TS), Castanea mollissima (CM), and Citrus reticulate (CR). One site was revegetated with Zenia insignis and Guimu-1 elephant grass (ZG), and one with only Guimu-1 elephant grass (GM). The remaining site, abandoned cropland (AC), was left to regenerate naturally. Here, we used Illumina sequencing of 16S rRNA genes to explore how the Grain for Green project affected soil bacterial community. We found that Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these soils. The dominant genera at each revegetation site were also different. The CM, ZI, TS, and AC sites were dominated by Micromonospora, ZG was dominated by Streptomyces, and CR and GM were dominated by Subgroup 6. The bacterial structure was most similar in AC and TS. Correlation analysis showed that the ratio of C:P had positive effects on KD4-96, Intrasporangiaceae, and Gaiella. The ratio of soil N:P was significantly positively correlated with Cupriavidus and Kribbella. The combination of planting Zenia insignis and Guimu-1 elephant grass had the best edaphic benefits, and the approach of planting Citrus reticulate and Toona sinensis needs to be improved. Redundancy analysis (RDA) revealed that plant Simpson index, and soil N:P contributed to 16 and 15.7% of the total variations in the soil bacterial community composition, respectively. Our results suggested that plant diversity (Simpson index) and soil stoichiometric ratio (N:P) were the important factors affecting the bacterial community, and phosphorus was the limiting factor of the bacterial community in the Grain for Green karst region. In the future, revegetation should be accompanied with phosphorus fertilizer and polycultures should be considered.

Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

Soil salinization limits crop growth and yield in agro-ecosystems worldwide by reducing soil health and altering the structure of microbial communities. Salt-tolerant plant growth-promoting rhizobacteria (PGPR) alleviate plant salinity stress. Wild soybean (Glycine soja Sieb. and Zucc.) is unique in agricultural ecosystems owing to its ability to grow in saline-alkali soils and fix atmospheric nitrogen via symbiotic interactions with diverse soil microbes. However, this rhizosphere microbiome and the nodule endosymbionts have not been investigated to identify PGPR. In this study, we investigated the structural and functional rhizosphere microbial communities in saline-alkali soil from the Yellow River Delta and coastal soil in China, as well as wild soybean root nodule endosymbionts. To reveal the composition of the microbial ecosystem, we performed 16S rRNA and nifH gene amplicon sequencing on root nodules and root zones under different environmental conditions. In addition, we used culture-independent methods to examine the root bacterial microbiome of wild soybean. For functional characterization of individual members of the microbiome and their impact on plant growth, we inoculated isolates from the root microbiome with wild soybean and observed nodulation. Sinorhizobium/Ensifer accounted for 97% of the root nodule microbiome, with other enriched members belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes; the genera Sphingomonas, Microbacterium, Arthrobacter, Nocardioides, Streptomyces, Flavobacterium, Flavisolibacter, and Pseudomonas; and the family Enterobacteriaceae. Compared to saline-alkali soil from the Yellow River Delta, coastal soil was highly enriched for soybean nodules and displayed significant differences in the abundance and diversity of β-proteobacteria, δ-proteobacteria, Actinobacteria, and Bacteroidetes. Overall, the wild soybean root nodule microbiome was dominated by nutrient-providing Sinorhizobium/Ensifer and was enriched for bacterial genera that may provide salt resistance. Thus, this reductionist experimental approach provides an avenue for future systematic and functional studies of the plant root microbiome.

Vital Members in the More Dysbiotic Oropharyngeal Microbiotas in H7N9-Infected Patients

The dysbiosis of oropharyngeal (OP) microbiota is associated with multiple diseases, including H7N9 infection. Different OP microbial colonization states may reflect different severities or stages of disease and affect the effectiveness of the treatments. Current study aims to determine the vital bacteria that could possibly drive the OP microbiota in the H7N9 patients to more severe microbial dysbiosis state. The OP microbiotas of 42 H7N9 patients and 30 healthy subjects were analyzed by a series of bioinformatics and statistical analyses. Two clusters of OP microbiotas in H7N9 patients, i.e., Cluster_1_Diseased and Cluster_2_Diseased, were determined at two microbial colonization states by Partition Around Medoids (PAM) clustering analysis, each characterized by distinct operational taxonomic units (OTUs) and functional metabolites. Cluster_1_Diseased was determined at more severe dysbiosis status compared with Cluster_2_Diseased, while OTU143_Capnocytophaga and OTU269_Treponema acted as gatekeepers for both of the two clustered microbiotas. Nine OTUs assigned to seven taxa, i.e., Alloprevotella, Atopobium, Megasphaera, Oribacterium, Prevotella, Stomatobaculum, and Veillonella, were associated with both H7N9 patients with and without secondary bacterial lung infection in Cluster_1. In addition, two groups of healthy cohorts may have potential different susceptibilities to H7N9 infection. These findings suggest that two OP microbial colonization states of H7N9 patients were at different dysbiosis states, which may help determine the health status of H7N9 patients, as well as the susceptibility of healthy subjects to H7N9 infection.

Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis

INTRODUCTION

Previous studies have largely explored the microbial composition and pathogenesis of pregnancy gingivitis. However, the patterns of microbial colonization during pregnancy in the absence of pregnancy gingivitis have rarely been studied. Characterization of the oral microbiome in pregnant women with healthy gingiva is an important initial step in understanding the role of the microbiome in progression to pregnancy gingivitis.

OBJECTIVES

In this study, we compared the oral microbiome of pregnant women without gingivitis (healthy pregnancy) with pregnant women having gingivitis and nonpregnant healthy women to understand how pregnancy modifies the oral microbiome and induces progression to pregnancy gingivitis.

METHODS

Subgingival plaque samples were collected from Chinese pregnant women with gingivitis (n = 10), healthy pregnant women (n = 10), and nonpregnant healthy women (n = 10). The Illumina MiSeq platform was used to perform 16S rRNA gene sequencing targeting the V4 region.

RESULTS

The alpha and beta diversity was significantly different between pregnant and nonpregnant women, but minimal differences were observed between pregnant women with and without gingivitis. Interestingly, the oral bacterial community showed higher abundance of pathogenic taxa during healthy pregnancy as compared with nonpregnant women despite similar gingival and plaque index scores. However, when compared with overt pregnancy gingivitis, pathogenic taxa were less abundant during healthy pregnancy. PICRUSt analysis (phylogenetic investigation of communities by reconstruction of unobserved states) also suggested no difference in the functional capabilities of the microbiome during pregnancy, irrespective of gingival disease status. However, metabolic pathways related to amino acid metabolism were significantly increased in healthy pregnant women as compared with nonpregnant women.

CONCLUSION

The presence of pathogenic taxa in healthy pregnancy and pregnancy gingivitis suggests that bacteria may be necessary for initiating disease development but progression to gingivitis may be influenced by the host environmental factors. More efforts are required to plan interventions aimed at sustaining health before the appearance of overt gingivitis.

KNOWLEDGE TRANSFER STATEMENT

The results of this study draw attention to the importance of oral health maintenance during pregnancy, as women without any prenatal oral conditions are predisposed to the risk of developing pregnancy gingivitis. Hence, it is important to incorporate comprehensive assessment of oral health in the prenatal health care schedules. Pregnant woman should be screened for oral risks, counseled on proper oral hygiene and expected oral changes, and referred for dental treatment, when necessary.

The complete chloroplast genome of Geodorum eulophioides (Orchidaceae)

Geodorum eulophioides Schltr., is a critically Endangered orchid (IUCN). In this study, we report the first complete chloroplast (cp) genome of G. eulophioides to provide the underlying information for genetic breeding and conservation studies of this species. The cp genome sequence of G. eulophioides is 149,466 bp in length, which contains one large single-copy region (LSC, 85,436 bp), one small single-copy region (SSC, 14,086 bp), and two inverted repeat regions (IRs, 24,972 bp). The cp genome encoded 177 genes, of which 106 were unique genes (78 protein-coding genes, 24 tRNAs, and 4 rRNAs). Phylogenetic analysis showed that G. eulophioides is closely related to the genera Eulophia.

The complete chloroplast genome of Musa beccarii

Musa becccarii N.W. Simmonds is one of the most important wild banana species native to Borneo. The chromosome number, 2n = 18, is new to the genus Musa. Wild populations of M. beccarii have been reduced enormously due to massive land clearing for oil palm plantations. In this study, we report the complete chloroplast genome of Musa beccarii by next-generation sequencing (NGS). The total length of the complete chloroplast genome was 168,457 bp, and the overall GC content of the whole genome is 36.8%. The cp genome of Musa beccarii contained a pair of inverted repeat regions of 34,819 bp, which were separated by the large single copy of 88,166bp and the small single copy of 11,059 bp. It encoded 114 genes, including 79 protein-coding genes, 31 tRNA genes, and 4 rRNA ribosomal genes. The most genes occur as a single copy, while 21 gene species occur in double copies. The phylogenetic analysis demonstrateds Musa becccarii formed a single branch among genus Musa. This complete chloroplast genome will provide important information for conservation and identification of species of Musa spp.

Illumina sequencing of complete chloroplast genome of Avicennia marina, a pioneer mangrove species

Mangrove tree Avicenna marina has great ecological significance in maintaining coastal ecosystem, but its unique potential for gene functions and genetic diversity underlying ecological adaptation remains investigation. In this study, the chloroplast genome of A. marina was first characterized by sequencing chloroplast DNA with Illumina technology. The A. marina genome was 147,909 bp in size with a typical quadripartite structure, which was deposited in GenBank under the accession number MT108381.

Silicate Fertilizer Amendment Alters Fungal Communities and Accelerates Soil Organic Matter Decomposition

Soil microorganisms play a crucial role in organic matter decomposition and nutrient cycling in cropping systems. Compared to bacteria, fungal community composition and the role of fungi in organic matter decomposition and nutrient cycling in agro-systems are, however, elusive. Silicon (Si) fertilization is essential to improve agronomic performance of rice. The effects of the Si fertilizer application on the soil fungal community composition and their contribution in soil organic matter (SOM) decomposition are not yet studied. We investigated the short-term (120 days) slag silicate fertilizer (SSF) amendment impacts on plant photosynthesis and soil biochemical changes, soil fungal communities (assessed by ITS amplicon illumina sequencing), hydrolytic and oxidase enzyme activities, CO₂ emissions, and bacterial and fungal respiration in diverse eco-geographic races of rice (Oryza sativa L.), i.e., Japonica rice (O. sativa japonica) and Indica rice (O. sativa indica). The short-term SSF amendment significantly increased the relative abundance of saprotrophic fungi and accelerated organic matter decomposition. The increase in saprotrophic fungi was mostly attributed to greater labile C availability and Si availability. Higher organic matter decomposition was accompanied by an increase in both hydrolytic and oxidative enzyme activities in response to the SSF amendment. The stimulation of oxidative enzyme activities was explained by an increase in root oxidase activities and iron redox cycling, whereas stimulation of hydrolytic enzyme activities was explained by the greater labile C availability under SSF fertilization. We conclude that the short-term SSF amendment increases saprotrophic fungal communities and soil hydrolytic and oxidative enzyme activities, which in turn stimulates SOM mineralization and thus could have negative feedback impacts on soil C storage in submerged rice paddies.

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Simple Summary

The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus.

Abstract

The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.

Complete chloroplast genome sequence of Pueraria thomsonii, an important traditional Chinese medicine plant

Pueraria thomsonii is a leguminous plant with high root yield and starch content. It is also a medicinal material in the Chinese pharmacopeia. However, the raw materials of P. thomsonii are often confused with some non-medicinal Pueraria plants. To enrich the genetic resources of P. thomsonii and guide its molecular identification, the complete chloroplast genome was sequenced and reported. The total genome of P. thomsonii is 153,434 bp in length. consisting of two inverted repeat regions (IRS, 25,640 bp each) separated by a large single-copy (LSC, 84,155 bp) and a small single-copy region (SSC, 17,999 bp). The overall GC content is 35.41%. It contains 130 genes, including 85 protein coding genes, 8 rRNA genes and 37 tRNA genes. Phylogenetic analysis showed that P. thomsonii could be distinguished from other plants and closely related to the legume Pachyrhizus erosus. This study enriches the genetic information of P. thomsonii and contributes to the screening of excellent germplasm.

The complete chloroplast genome sequence of Blastus pauciflorus (Melastomataceae)

Blastus pauciflorus, a shrub endemic to Hong Kong and Guangdong, south China, growing on low-altitude hillsides, under the forest. The species is controversial in classification. Herein, we report the complete chloroplast genome sequence assembled from Illumina pair-end sequencing data, with aims to resolve its relationship with the related species. The complete chloroplast genome was 155,983 bp in length, includes two inverted repeat regions (IRs) of 26,716 bp each, which were separated by a large single copy region (LSC) 86,101 bp and a small single copy region (SSC) 16,450 bp. The chloroplast genome contained 129 genes, including 82 protein-coding genes, 2 pseudogenes, 37 tRNA genes and 8 rRNA genes. The overall GC content in the chloroplast genome of B. pauciflorus was 37.0%. Phylogenetic analysis showed that B. pauciflorus is closed to B. cochinchinensis.

The chloroplast genome of silk floss tree (Ceiba speciosa)

Ceiba speciosa (Malvaceae), also called silk floss tree, is a beautiful and deciduous tree native to tropical and subtropical forests of South America. Its phylogenetic position remains unclear. In this study, the complete chloroplast genome sequence of C. speciosa was reported. Its chloroplast genome size was 160,360 bp, which contains a small single copy (SSC) region of 19,947 bp and a large single copy region (LSC) of 89,393 bp, and two inverted repeats (IRs) of 25,510 bp each. In total, 129 genes were annotated for the chloroplast genome, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis showed that C. speciosa was sister to Bombax ceiba.

The complete chloroplast genome sequence of Ludisia discolor from Hainan of China

Ludisia discolor is one of the most important ornamental and medicinal orchids. To improve our understanding of the evolution of chloroplast, we resequenced complete chloroplast (cp) genome of L. discolor from Hainan, China. The cp genome sequence of L. discolor of Hainan was 153,324 bp in length, with a large single-copy (LSC) region of 82,922 bp, a small single-copy (SSC) region of 17,258 bp, and a pair of inverted repeats (IR) regions of 26,572 bp. Complete chloroplast genome contain 132 genes, there were 86 protein-coding genes, 38 tRNA genes and eight rRNA genes. The phylogenetic tree showed that L. discolor of Hainan is sister to L. discolor (unknown distributed region). Their cp genomes have same gene number but different in length of genome, indicating high conserved among them.

The complete chloroplast genome of Codonopsis tsinglingensis (Campanulaceae), an endemic Chinese medicine species in Qinling mountains

Codonopsis tsinglingensis, belonging to the Campanulaceae family, is a perennial medicinal herb highly valued in Chinese traditional medicine. The complete chloroplast genome of C. tsinglingensis was sequenced using the Illumina Hiseq 4000 platform. The size of the C. tsinglingensis chloroplast genome is 170,253 bp, with an average GC content of 38.3%. This circular molecule has a typical quadripartite structure containing a large single copy (LSC) region of 85,408 bp, a small single copy (SSC) region of 8179 bp, and two inverted (IRs) repeat regions of 38,333 bp. The genome contains 138 genes, including 92 protein-coding genes, 38 transfer RNA genes (tRNA), 8 ribosomal RNA genes (rRNA). Phylogenetic analysis based on complete chloroplast genome sequences of 14 species indicates that C. tsinglingensisis closely related to Codonopsis minima in the Campanulaceae family.

Characterization of the complete plastome of Ophrys aveyronensis, a Euro-Mediterranean orchid with an intriguing disjunct geographic distribution

Ophrys aveyronensis is an orchid with disjunct geographic distribution. For biogeographic and conservation purpose, we sequenced its complete plastome using Illumina data. The complete plastome is 146,816 bp in length, consisting of a pair of inverted repeats (IRs) of 25,006 bp, a large single-copy (LSC) region and a small single-copy region (SSC) of 80,495 and 16,309 bp, respectively. It was found to contain 133 genes, including 86 protein-coding genes, up to 39 trRNA genes and 8 rRNA genes. The overall GC content of the plastid genome is 36.9%. Phylogenetic inference confirms that O. aveyronensis is very close to O. sphegodes.

The complete chloroplast genome of Symphoricarpos orbiculatus (Caprifoliaceae), an important ornamental plant

Symphoricarpos orbiculatus is an important landscape and ornamental plant. In this study, we report the complete chloroplast genome sequences of S. orbiculatus. The complete chloroplast genome of S. orbiculatus was 156,044 bp in length. The genome has a typical quadripartite structure, including a large single-copy (LSC) region of 88,756 bp, a small single-copy (SSC) region of 19,130 bp, and two inverted repeat (IR) regions of 24,079 bp each. Overall, the GC content was 38.4%. In the genome, it was identified to comprise130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This study provides valuable information for molecular phylogenetic study of Caprifoliaceae and is significant for variety development of Symphoricarpos.

DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors

Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%–40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.

Profiling the Functional Diversity of Termite Mound Soil Bacteria as Revealed by Shotgun Sequencing

Profiling the metabolic processes performed by bacteria is vital both for understanding and for manipulating ecosystems for industrial or research purposes. In this study we aim to assess the bacterial functional diversity in termite mound soils with the assumption that significant differences will be observed in the functional diversity of bacteria between the termite mound soils and their surrounding soils and that each environment has a distinguishing metabolic profile. Here, metagenomic DNA extracted from termite mound soils and their corresponding surrounding soils, which are 10 m apart, were sequenced using a shotgun sequencing approach. Our results revealed that the relative abundances of 16 functional categories differed significantly between both habitats. The α diversity analysis indicated no significant difference in bacterial functional categories within the habitats while the β diversity showed that the bacterial functional categories varied significantly between the termite mound soils and the surrounding soil samples. The variations in soil physical and chemical properties existing between the two environments were held accountable for the differences in bacterial functional structure. With the high relative abundance of functional categories with unknown function reported in this study, this could signify the likelihood of getting novel genes from termite mound soils, which are needed for research and commercial applications.

Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China

While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.

Isolation, Characterization, and Genomic Analysis of Pseudomonas sp. Strain SMT-1, an Efficient Fluorene-Degrading Bacterium

Comprehensive study of novel microbial organisms capable of degrading fluorene is crucial to develop essential strategies for further application on enhanced bioremediation technologies. Many fluorene-degrading bacteria have been studied; however, little information about the genome sequences of these organisms, which would facilitate investigation of the molecular mechanisms of fluorene degradation, is available. In this study, a bacterial strain designated SMT-1, which uses fluorene as its sole carbon source, was isolated from Laogang landfill in Shanghai, People’s Republic of China, and identified as a Pseudomonas sp., based on 16S rRNA gene sequence analysis. Maximum growth and degrading activity of strain SMT-1 were observed at 30°C, pH 7.0 and 200 r/min in mineral salt medium containing 0.4 mm fluorene. We obtained a draft genome sequence of strain SMT-1 to gain insight into the genetic mechanisms for the degradation of aromatic compounds. Sequences greater than 1 kb in length were obtained by Illumina sequencing; strain SMT-1 was found to contain 5542 predicted genes. This working draft genome comprises 68 contigs and DNA scaffolds and has a total size of 6 108 237 bp and a calculated G + C content of 61.59%. Amino acid metabolism clusters were enriched in SMT-1 genes annotation, with the highest abundant observed for the “ABC transporters” subcategories, followed by transcription, energy production and conversion, and inorganic ion transport and metabolism. The genomic information for SMT-1 provides a useful resource for elucidating the molecular mechanism of fluorene catabolism.

Development of Polymorphic Simple Sequence Repeat Markers using High-Throughput Sequencing in Button Mushroom (Agaricus bisporus)

The white button mushroom (Agaricus bisporus) is one of the most widely cultivated species of edible mushroom. Despite its economic importance, relatively little is known about the genetic diversity of this species. Illumina paired-end sequencing produced 43,871,558 clean reads and 69,174 contigs were generated from five offspring. These contigs were subsequently assembled into 57,594 unigenes. The unigenes were annotated with reference genome in which 6,559 unigenes were associated with clusters, indicating orthologous genes. Gene ontology classification assigned many unigenes. Based on genome data of the five offspring, 44 polymorphic simple sequence repeat (SSR) markers were developed. The major allele frequency ranged from 0.42 to 0.92. The number of genotypes and the number of alleles ranged from 1 to 4, and from 2 to 4, respectively. The observed heterozygosity and the expected heterozygosity ranged from 0.00 to 1.00, and from 0.15 to 0.64, respectively. The polymorphic information content value ranged from 0.14 to 0.57. The genetic distances and UPGMA clustering discriminated offspring strains. The SSR markers developed in this study can be applied in polymorphism analyses of button mushroom and for cultivar discrimination.

Complete Genome of Bacillus subtilis subsp. subtilis KCTC 3135T and Variation in Cell Wall Genes of B. subtilis Strains

The type strain Bacillus subtilis subsp. subtilis KCTC 3135^T was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggest that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

Metabolic Syndrome During Perinatal Period in Sows and the Link With Gut Microbiota and Metabolites

In humans, the metabolic and immune changes occurring during perinatal period also describe metabolic syndrome. Gut microbiota can cause symptoms of metabolic syndrome in pregnant women. Increased gut permeability is also involved in metabolic disorders in non-pregnant hosts. However, longitudinal studies investigating the changes in metabolic characteristics, gut microbiota, and gut permeability of sows throughout pregnancy and lactation are lacking. The correlation between gut microbiota and metabolic status of sows is also poorly known. The present study was conducted to investigate the temporal variations in sow metabolic characteristics, gut microbiota, gut permeability, and gut inflammation at days 30 (G30) and 109 (G109) of gestation and days 3 (L3) and 14 (L14) of lactation. Results showed that insulin sensitivity was decreased in L3. Circulating concentrations of pro-inflammatory cytokine IL-6 increased in G109 and L3. 16S rRNA gene sequencing of the V3-V4 region showed that gut microbiota changed dramatically across different reproductive stages. The bacterial abundance and alpha diversity in L3 were the lowest. The phyla Proteobacteria and Fusobacteria exhibited the highest relative abundance in L3. Among the genera, Bacteroides, Escherichia_Shigella, and Fusobacterium were highest, but Oscillospira the lowest, in relative abundance in L3. The fecal levels of acetate and total short-chain fatty acids were increased in G109, but fecal butyrate concentrations were markedly decreased in L3. The plasma zonulin concentrations, a biomarker for gut permeability, were increased in G109 and L3. The plasma endotoxin concentrations were increased in L3. Furthermore, levels of fecal lipocalin-2 and pro-inflammatory cytokines IL-6 and TNF-α were increased in G109 and L3. In contrast, fecal levels of anti-inflammatory cytokine IL-10 were significantly decreased in G109 and L3. Additionally, the increased relative abundances of Fusobacterium in L3 were positively correlated with plasma zonulin and fecal endotoxin but negatively correlated with fecal IL-10. These findings indicate that the mother sow exhibits a metabolic syndrome and dramatical changes in gut microbiota during perinatal period, especially in early lactation. Besides, increased gut permeability and plasma endotoxin concentrations caused by negative microbial changes would possibly be the potential mechanisms under which sow’s metabolic disorders and inflammatory status were exacerbated during early lactation.

Complete plastome sequence of Nepenthes mirabilis (Nepenthaceae): a "vulnerable" herb in China

Nepenthes mirabilis (Nepenthaceae) is an erect or climbing (0.5–2 m tall) herb distributed in Africa (Madagascar), south and southeast Asia, North Australia and Pacific Islands (Caroline Islands). There is only one species in China. It grows in wet and sandy soils places throughout forests, grasslands, swamps, mountains, roadsides, wastelands having altitudes that sea level to 400 m. It has been ranked as a VU (Vulnerable) species in China. Here we report and characterize the complete plastid genome sequence of N. mirabilis in an effort to provide genomic resources useful for its conservation. The complete plastome is 155,755 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,415 bp, a Large Single-Copy (LSC) region of 84,997 bp and a Small Single-Copy (SSC) region of 17,928 bp. The plastome contains 113 genes, consisting of 77 unique protein-coding genes, three pseudogenes, 29 unique tRNA genes, and four unique rRNA genes. The overall A/T content in the plastome of N. mirabilis is 62.8%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc., and we determined that N. mirabilis 32 and Dionaea muscipula were closely related. The complete plastome sequence of N. 33 mirabilis will provide a useful resource for the conservation genetics of this species as 34 well as for the phylogenetic studies in Caryophyllales.

De Novo Assembly and Analysis of the White-Backed Planthopper (Sogatella furcifera) Transcriptome

The white-backed planthopper Sogatella furcifera (Horváth) has become an important pest on rice in China and Southeast Asian countries. White-backed planthopper wing bud length is in relation to adult wing length, but little is known about the development and differentiation of wing buds at the molecular level. Using Illumina HiSeq high-throughput sequencing technology, we sequenced four cDNA libraries, two biological replicates of long-winged female fifth-instar nymphs (LW), and two of short-winged nymphs (SW). In total, 62,154 unigenes with an average length of 984 bp and N50 length of 1,878 bp were obtained by de novo transcriptome assembly. A total of 18,416 open reading frames (ORFs) were predicted based on the unigenes. Ninety-three percentage of these ORFs could be annotated by searching for homology in six protein databases. A total of 184 differentially expressed genes (DEGs) with 129 upregulated and 55 downregulated were found in SW compared to LW. Gene Ontology and euKaryotic Orthologous Group classification provided comprehensive information about the function of each gene. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed five enriched pathways including three metabolic pathways. In addition, we found that some DEGs were relevant to muscle movement and cuticle and likely involved in development and differentiation of wing buds. This study provided transcriptome resource of female fifth-instar nymphs of white-backed planthopper including long-winged and short-winged nymphs, and different molecular features between them lay the foundation for adult wing morph prediction, promoting further studies on planthopper population management.

Complete plastome sequence of Dracaena cambodiana (Asparagaceae): a species considered "Vulnerable" in Southeast Asia

Dracaena cambodiana (Asparagaceae) is a treelike plant ranging from 3 to 10 m tall. It grows in low-elevation forests (0-300 m) having dry and sandy soils. It is distributed in Southern Hainan Island in China and other Southeast Asian countries (e.g. Cambodia, Laos, Thailand and Vietnam). The dried resin can be used medicinally as a substitute for that of Dracaena cochinchinensis. It has been ranked as a Vulnerable (VU) species in China. Here we report and characterize the complete plastid genome sequence of D. cambodiana. The complete plastome is 156,697 bp in length. It contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,526 bp, a Large Single-Copy (LSC) region of 84,988 bp and a Small Single-Copy (SSC) region of 18,657 bp. The plastome contains 113 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, four unique rRNA genes and three pseudogenes (i.e. matK, infA, ndhF). The overall A/T content in the plastome of D. cambodiana is 62.4%. We performed phylogenetic analyses using the entire plastome, including spacers, introns, etc., and we determined that D. cambodiana and Maianthemum bicolor were closely related. The complete plastome sequence of D. cambodiana will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Asparagales.

The complete chloroplast genome of the endangered species Triaenophora shennongjiaensis (Orobanchaceae s.l.)

Triaenophora shennongjiaensis (Orobanchaceae sensu lato) is a recently described rare and endangered species endemic to Central China. In this study, the complete chloroplast (cp) genome of T. shennpongjiaensis was assembled based on reads obtained with the Illumina HiSeq platform. The cp genome of T. shennongjiaensis was 15,5319 bp in length and contained a pair of inverted repeat (IR, 27,484 bp) regions separated by a small single copy (SSC, 15,450 bp) and a large single copy (LSC, 84,901 bp) region. It encoded 112 genes including 78 protein-coding genes, 30 tRNA genes, and eight ribosomal RNA genes. The overall AT content of T. shennongjiaensis cp genome is 61.9%. The maximum likelihood phylogenetic analysis supports T. shennongjiaensis as sister to Rehmannia. This result will be helpful for the systematics, conservation, and breeding programs of Triaenophora.