Effects of salt concentration on microbial diversity and volatile compounds during suancai fermentation.

Suancai is a popular fermented product of Brassica vegetable in China. As important additive, salt concentration has crucial effects on the quality of suancai. To investigate the effects of salt concentration on suancai fermentation, the microbial diversity and volatile compounds (VCs) during fermentation were investigated by using Illumina HiSeq sequencing and GC-MS. Firmicutes, Proteobacteria and Ascomycota were detected as the main phylum during the fermentation with different salt concentrations. Lactobacillus, Lactococcus, Klebsiella, Weissella, Pediococcus, Candida, Cladosporium, Gibberella, Aspergillus, etc., were detected were observed during the fermentation with different concentrations. After fermentation, Lactobacillus predominated the fermentation of suancai and was not affected by salt concentration. Pediococcus, Leuconostoc, Weissella, Sporobolomyces, Azospirillum, Klebsiella, Acinetobacter and Cladosporium were significant affected by salt concentration. Salt addition could affect the VCs profiles and reduce the isothiocyanates after fermentation. Seventy-nine VCs were detected and strongly correlated with the dominant genus Lactobacillus during suancai fermentation. The inoculated fermentation of Lactobacillus could improve the VCs during fermentation. In conclusion, 6% salt addition could acquire a higher Lactobacillus abundance and a better taste quality. These results may facilitate the understanding of the effect of salt concentration on the fermentation ecology to improve suancai characteristics.

Silicon application and related changes in soil bacterial community dynamics reduced ginseng black spot incidence in Panax ginseng in a short-term study.

BACKGROUND: This study analyzed the effect of silicon (Si) application on the occurrence of ginseng black spot caused by Alternaria panax. We explored the differences in soil physical and chemical factors and microbial community structure following Si application as well as the key factors that affected the occurrence of ginseng black spot in soil. Potted Panax ginseng plants were used to assess the effect of Si treatment on ginseng black spot. Soil physical and chemical properties were comprehensively analyzed. Bacterial communities were analyzed using Illumina HiSeq sequencing targeting the 16S rRNA gene. RESULTS: After inoculation with A. panax, the morbidity (and morbidity index) of ginseng with and without Si was 52% (46) and 83% (77), respectively. Soil physical and chemical analysis showed that under the ginseng black spot inoculation, bacterial communities were mainly affected by pH and available potassium, followed by ammonium nitrogen and available Si. NMDS and PLS-DA analyses and the heat maps of relative abundance revealed that Si application elevated the resistance of ginseng black spot as regulated by the abundance and diversity of bacterial flora in rhizosphere soils. Heatmap analysis at the genus level revealed that A. panax + Si inoculations significantly increased the soil community abundance of Sandaracinus, Polycyclovorans, Hirschia, Haliangium, Nitrospira, Saccharothrix, Aeromicrobium, Luteimonas, and Rubellimicrobium and led to a bacterial community structure with relative abundances that were significantly similar to that of untreated soil. CONCLUSIONS: Short-term Si application also significantly regulated the structural impact on soil microorganisms caused by ginseng black spot. Our findings indicated that Si applications may possibly be used in the prevention and treatment of ginseng black spot.

Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour.

BACKGROUND: Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development. RESULTS: In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a). CONCLUSION: Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.

Deciphering the differences of bacterial communities between high- and low-productive wheat fields using high-throughput sequencing.

Microbial communities have been demonstrated to be essential for healthy and productive soil ecosystems. However, an understanding of the relationship between soil microbial community and soil productivity levels is remarkably limited. In this study, bulk soil (BS), rhizosphere soil (RS), and root (R) samples from the historical high-productive (H) and low-productive (L) soil types of wheat in Hebei province of China were collected and analyzed by high-throughput sequencing. The study highlighted the richness, diversity, and structure of bacterial communities, along with the correlation networks among different bacterial genera. Significant differences in the bacterial community structure between samples of different soil types were observed. Compared with the low-productive soil type, the bacterial communities of samples from the high-productive soil type possessed high species richness, low species diversity, complex and stable networks, and a higher relative abundance of beneficial microbes, such as Pseudoxanthomonas, unclassified Vicinamibacteraceae, Lysobacter, Massilia, Pseudomonas, and Bacillus. Further analysis indicated that the differences were mainly driven by soil organic matter (SOM), available nitrogen (AN), and electrical conductivity (EC). Overall, the soil bacterial community is an important factor affecting soil health and crop production, which provides a theoretical basis for the targeted regulation of microbes in low-productivity soil types.

Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China.

Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems.

Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing.

"Yibin Baijiu" (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production.

Comparison of cyanobacterial communities in temperate deserts: A cue for artificial inoculation of biological soil crusts.

The topsoil cyanobacteria in biological soil crusts (BSCs) play a vital role in stabilizing soil surface of disturbed habitats in water and nutrient-poor ecosystems. Currently, artificial inoculation of BSCs is considered as an effective approach to restore habitats and accelerate ecosystem regeneration. Understanding the character of cyanobacterial communities is the necessary prerequisite to explore the artificial inoculation of BSCs. For this reason, cyanobacterial communities in BSCs were compared between two mid-latitute temperate deserts with distinct precipitation patterns. The results showed that Oscillatoriales and Nostocales dominated crusts in the Tengger desert with majority of rainfall in summer and early autumn while Oscillatoriales dominated crusts in the Kyzyl kum desert with more rainfall in winter and early spring. Moreover, filamentous Microcoleus vaginatus overwhelmingly dominated all the crusts in both deserts with Mastigocladopsis sp. and Chroococcidiopsis spp. as the dominant heterocystous cyanobacteria. Of note, genus Wilmottia kept a relative stable and high abundance in both deserts. The top two abundantly shared cyanobacteria (> 1% of total sequences) were M. vaginatus and Mastigocladopsis sp. in both deserts, while 16 genera with significant variances were found between the two deserts (P <0.05). Total variations of cyanobacterial communities across the deserts were largely explained by a combination of biotic factors (microbial biomass C and N) and abiotic factors (soil pH, soil water content, soil water holding capacity, and soil available potassium). Compared to better-developed crusts, cyanobacterial abundance was higher in cyanobacterial crusts. BSC type and/or geographic location significantly affected cyanobacterial Shannon diversity without significantly influencing species richness. Our data suggest that the basic and major groups (e.g. M. vaginatus, Wilmottia spp., Mastigocladopsis sp., and Chroococcidiopsis spp.), and the abundantly shared phylotypes which showed significant difference in cyanobacterial communities between deserts, should be focused on to further explore the artificial inoculation of BSCs in temperate drylands.

Characterization of Gut Microbiome in the Mussel Mytilus galloprovincialis in Response to Thermal Stress.

The gut microbiota is essential for utilization of energy and nutrition and may have a role in host immunity in response to environmental shifts. The present study evaluated the temperature stress (increasing from 21 to 27°C) on gut microbiome and dynamics of the mussel Mytilus galloprovincialis by 16S rRNA gene sequencing with the aim of discovering the gut microbiome resilience to warming. Exposure to high temperature of 27°C significantly reduced the survival of M. galloprovincialis associated with increased microbial diversity of gut. The microbial communities were shifted with elevated temperature (from 21 to 27°C) and different exposure time (from day 0 to day 7) by principal coordinate analysis (PCoA). Linear discriminant analysis effect size (LEfSe) revealed that the relative abundance of Vibrio and Arcobacter presented in live animals as the top genus-level biomarkers during the initial exposure to 27°C and followed by microbiomes fluctuation with increasing exposure time at day 4 and day 7. The proliferation of opportunistic pathogens such as genus Vibrio and Arcobacter might increase host susceptibility to disease and contributed greatly to mortality. The results obtained in this study provide the knowledge on ecological adaptation for south domestication of M. galloprovincialis and host-bacteria interaction during temperature stress (27°C).

High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T.

The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of Geobacillus uzenensis (DSM 23175T), G. thermocatenulatus (DSM 730T) and Parageobacillus galactosidasius (DSM 18751T). Phylogenomic analyses revealed that DSM 18751T and DSM 23175T represent later heterotypic synonyms of P. toebii and G. subterraneus, respectively, while DSM 730T represents the type strain for the species G. thermocatenulatus. These genome sequences will contribute towards a deeper understanding of the ecological and biological diversity and the biotechnological exploitation of the 'geobacilli'.

Different Selectivity in Fungal Communities Between Manure and Mineral Fertilizers: A Study in an Alkaline Soil After 30 Years Fertilization.

Fertilizer application has contributed substantially to increasing crop yield. Despite the important role of soil fungi in agricultural production, we still have limited understanding of the complex responses of fungal taxonomic and functional groups to organic and mineral fertilization in long term. Here we report the responses of the fungal communities in an alkaline soil to 30-year application of mineral fertilizer (NP), organic manure (M) and combined fertilizer (NPM) by the Illumina HiSeq sequencing and quantitative real-time PCR to target fungal internal transcribed spacer (ITS) genes. The results show: (1) compared to the unfertilized soil, fertilizer application increased fungal diversity and ITS gene copy numbers, and shifted fungal community structure. Such changes were more pronounced in the M and NPM soils than in the NP soil (except for fungal diversity), which can be largely attributed to the manure induced greater increases in soil total organic C, total N and available P. (2) Compared to the unfertilized soil, the NP and NPM soils reduced the proportion of saprotrophs by 40%, the predominant taxa of which may potentially affect cellulose decomposition. (3) Indicator species analysis suggested that the indicator operational taxonomic units (OTUs) in the M soil occupied 25.6% of its total community, but that only accounted for 0.9% in the NP soil. Our findings suggest that fertilization-induced changes of total fungal community were more responsive to organic manure than mineral fertilizer. The reduced proportion of cellulose decomposition-related saprotrophs in mineral fertilizer treatments may potentially contribute to increasing their soil C stocks.

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda.

The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia-Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia-Shigella.

Response of the microbial community structure of biofilms to ferric iron in microbial fuel cells.

Ferric iron can affect the current generation of microbial electrochemical system (MES); however, how it influences microbial biofilm formation and metabolic activity has not been reported. Here, we describe the response of microbial electrode biofilm communities to insoluble ferric iron (Fe3+) at different concentrations in microbial fuel cells (MFCs). Insoluble ferric iron (200µM) improved electrochemical activity of the MFCs microbial biofilms during start-up and resulted in a higher maximum power density of 0.95W/m2, compared with the control (0.76W/m2), 500µM Fe3+ (0.83W/m2), 1000µM Fe3+ (0.73W/m2), and 2000µM Fe3+ (0.59W/m2) treatments. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that the predominant populations in the anode biofilms of the MFCs belonged to Geobacter, with relative abundance of 66-75%. Microbial cathode biofilm communities were more susceptible to Fe3+, as an obvious shift in the cathode biofilm community structures occurred as Fe3+ concentration was increased. The most predominant populations in the MFC cathode biofilms without Fe3+ and with 200µM Fe3+ were affiliated with Thauera (46% and 35%), whereas no absolutely predominant populations were present in the MFC cathode biofilm with 1000µM Fe3+. The results demonstrate that a low concentration of Fe3+ facilitated the power output of MFCs and shaped community structures of the electrode biofilm.

Diversity of Fungal Communities in Heshang Cave of Central China Revealed by Mycobiome-Sequencing.

Deciphering of the mycobiome in pristine karst caves has been impeded by constraints of remote locations, inaccessibility to specimens and technical limitations, which greatly restricted in-depth understanding of mycobiomes in subterranean ecosystem. Here, mycobiomes of Heshang Cave in south-western karst region of China were investigated by Illumina HiSeq sequencing of fungal rRNA-ITS1 gene across different habitats. In total 793,502 ITS1 reads and 2,179 OTUs from 778 Mb reads after stringent quality control (Q30) and 453 genera, 72 orders and 19 classes within 6 phyla were detected. Ascomycota (42% OTUs) dominated across the five habitats. Shannon-Wiener index varied from 1.25 to 7.62 and community richness was highest in drip waters, followed by weathered rocks, bat guanos, sediments, and air samples. Mycobiomes displayed specificity to five habitats and more distinct OTUs were found in weathered rocks (12%) and drip waters (9%). In contrast, only 6.60% core OTUs were shared by five habitats. Notably, weathered rocks possessed more indicator groups and were revealed for the first time to be dominated by Sordariomycetes (43%). The community richness of air mycobiomes increased from cave entrance to the innermost part and dominated by the indicator groups of Penicillium mallochii (>30%) and P. herquei (>9%). Our work represents the largest attempt to date to a systematical investigation of oligotrophic solution-cave-associated mycobiomes in China. Our discovery of high diversity of mycobiomes in Heshang Cave also suggests that eukaryotic microorganisms may play a crucial role in subsurface environments.

Soil pH Is the Primary Factor Correlating With Soil Microbiome in Karst Rocky Desertification Regions in the Wushan County, Chongqing, China.

Karst rocky desertification (KRD) is a process of land degradation, which causes desert-like landscapes, deconstruction of endemic biomass, and declined soil quality. The relationship of KRD progression with above-ground communities (e.g. vegetation and animal) is well-studied. Interaction of soil desertification with underground communities, such as soil microbiome, however, is vastly unknown. This study characterizes change in soil bacterial community in response to KRD progression. Soil bacterial communities were surveyed by deep sequencing of 16S amplicons. Eight soil properties, pH, soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK), were measured to assess soil quality. We find that the overall soil quality decreases along with KRD progressive gradient. Soil bacterial community compositions are distinguishingly different in KRD stages. The richness and diversity in bacterial community do not significantly change with KRD progression although a slight increase in diversity was observed. A slight decrease in richness was seen in SKRD areas. Soil pH primarily correlates with bacterial community composition. We identified a core microbiome for KRD soils consisting of; Acidobacteria, Alpha-Proteobacteria, Planctomycetes, Beta-Proteobacteria, Actinobacteria, Firmicutes, Delta-Proteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Gemmatimonadetes in this study. Phylum Cyanobacteria is significantly abundant in non-degraded soils, suggesting that Cyanobacterial activities might be correlated to soil quality. Our results suggest that Proteobacteria are sensitive to changes in soil properties caused by the KRD progression. Alpha- and beta-Proteobacteria significantly predominated in SKRD compared to NKRD, suggesting that Proteobacteria, along with many others in the core microbiome (Acidobacteria, Actinobacteria, Firmicutes, and Nitrospirae), were active in nutrient limiting degraded soils. This study demonstrates the relationship of soil properties with bacterial community in KRD areas. Our results fill the gap of knowledge on change in soil bacterial community during KRD progression.

Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.

BACKGROUND: Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. RESULTS: Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. CONCLUSIONS: Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms.