In vitro Inoculation of Fresh or Frozen Rumen Fluid Distinguishes Contrasting Microbial Communities and Fermentation Induced by Increasing Forage to Concentrate Ratio

In vitro rumen batch culture is a technology to simulate rumen fermentation by inoculating microorganisms from rumen fluids. Although inocula (INO) are commonly derived from fresh rumen fluids, frozen rumen fluids are also employed for the advantages of storing, transporting, and preserving rumen microorganisms. The effects of frozen INO on microbial fermentation and community may be interfered with by substrate type, which has not been reported. This study was designed to test whether rumen fluid treatments (i.e., fresh and frozen) could interact with incubated substrates. A complete block design with fractional arrangement treatment was used to investigate the effects of INO (fresh or frozen rumen fluids) and concentrate-to-forage ratios (C/F, 1:4 or 1:1) on rumen fermentation and microbial community. The effects of increasing C/F were typical, including increased dry matter (DM) degradation and total volatile fatty acids (VFA) concentration (P < 0.001), and decreased acetate to propionate ratio (P = 0.01) and bacterial diversity of richness and evenness (P ≤ 0.005) with especially higher fermentative bacteria such as genus Rikenellaceae_RC, F082, Prevotella, Bacteroidales_BS11, Muribaculaceaege, and Christensenellaceae_R-7 (P ≤ 0.04). Although frozen INO decreased (P < 0.001) DM degradation and altered rumen fermentation with lower (P ≤ 0.01) acetate to propionate ratio and molar proportion of butyrate than fresh INO, typical effects of C/F were independent of INO, as indicated by insignificant INO × C/F interaction on substrate degradation, VFA profile and bacterial community (P ≥ 0.20). In summary, the effect of C/F on fermentation and bacterial diversity is not interfered with by INO type, and frozen INO can be used to distinguish the effect of starch content.

Environmental factors shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench

Hailed as "The Fourth Pole", the Mariana Trench is the deepest part of the ocean. The microbial diversity in it is extremely complicated, which might be caused by the unique environmental factors such as high salinity, low temperature, high hydrostatic pressure, and limited nutrition. Based on 4 seawater samples and 4 sediment samples obtained from the Mariana Trench, we isolated and fostered the microorganism clones with kinds of culture mediums and high-throughput culturing. By using the molecular identification methods based on PCR of 16S rDNA and ITS gene, 1266 bacterial strains in total were isolated and identified, which affiliated to 7 classes, 16 orders, 25 families and 36 genera in four phyla：Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Strains in genera Halomonas, Pseudoaltermonas were the dominant bacteria isolated from the samples. With Mantel tests on the sample-environmental parameter matrix, the sample-environmental organic matter diversity matrix and the sample-microbial diversity matrix, we concluded that the environmental parameters and the organic matters in the condition can shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench.

Comparative Microbiomes of the Respiratory Tract and Joints of Feedlot Cattle Mortalities

A comparative study of microbiota of the respiratory tract and joints of bovine respiratory disease (BRD) cattle mortalities was undertaken. Nasopharynx, trachea, lung and joint samples were collected from 32 cattle that died of BRD, “cases”, and 8 that died of other causes, “controls”. Bacterial diversity was lower (p < 0.05) in the nasopharynx, trachea and lungs of cases as compared to controls. In cases, alpha-diversity (p < 0.05) was lower in the lungs and joints than the nasopharynx. Proteobacteria, Tenericutes, Bacteroidetes, Firmicutes and Actinobacteria were the most abundant phyla in all samples. Relative abundances of Mycoplasma spp. in the lung, Pasteurella spp. in the trachea and lung, and Histophilus spp. in the lung, trachea and nasopharynx of cases were higher (p < 0.001) than controls. Mycoplasma spp. comprised 20.5% of bacterial flora in the joint, 36.0% in the lung, 22.4% in the trachea and 8.8% in the nasopharynx. Mannheimia spp. (21.8%) and Histophilus spp. (10.4%) were more abundant in lungs. Cattle that died of BRD possessed less diverse respiratory microbiomes with a higher abundance of respiratory pathogens. Mycoplasma spp. were prominent members of pneumonic lungs and joints displaying septic arthritis.

Efficiency and bacterial diversity of an improved anaerobic baffled reactor for the remediation of wastewater from alkaline-surfactant-polymer (ASP) flooding technology

Alkaline-surfactant-polymer (ASP) flooding technology is used to maximize crude oil recovery. However, the extensive use of alkaline materials makes it difficult to treat the water used. Here, an improved multi-zone anaerobic baffled reactor (ABR) using FeSO4 as electron acceptor was employed to treat the wastewater from ASP flooding technology, and the effects on major pollutants (hydrolyzed polyacrylamide, petroleum substances, surfactants suspended solids) and associated parameters (chemical oxygen demand, viscosity) were evaluated. Gas chromatography-mass spectrometry (GC-MS) was used to follow the degradation and evolution of organic compounds while high-throughput DNA sequencing was used to determine the bacterial diversity in the ABR. The results obtained after 90 d of operation showed decreases in all parameters measured and the highest mean removal rates were obtained for petroleum substances (98.8%) and suspended solids (77.0%). Amounts of petroleum substances in the ABR effluent could meet the requirements of a national standard for oilfield reinjection water. GC-MS analysis showed that a wide range of chemicals (e.g. aromatic hydrocarbons, esters, alcohols, ketones) could be sequentially removed from the influent by each zone of ABR. The high-throughput DNA sequencing showed that the bacteria Micropruina, Saccharibacteria and Synergistaceae were involved in the degradation of pollutants in the anaerobic and anoxic reaction zones, while Rhodobacteraceae and Aliihoeflea were the main functional microorganisms in the aerobic reaction zones. The results demonstrated that the improved ABR reactor had the potential for the treatment of wastewater from ASP flooding technology.

Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.