Probiotics/prebiotics have the ability to modulate the balance and activities of the gastrointestinal (GI) microbiota, and are, thus, considered beneficial to the host animal and have been used as functional foods. Numerous factors, such as dietary and management constraints, have been shown to markedly affect the structure and activities of gut microbial communities in livestock animals. Previous studies reported the potential of probiotics and prebiotics in animal nutrition; however, their efficacies often vary and are inconsistent, possibly, in part, because the dynamics of the GI community have not been taken into consideration. Under stressed conditions, direct-fed microbials may be used to reduce the risk or severity of scours caused by disruption of the normal intestinal environment. The observable benefits of prebiotics may also be minimal in generally healthy calves, in which the microbial community is relatively stable. However, probiotic yeast strains have been administered with the aim of improving rumen fermentation efficiency by modulating microbial fermentation pathways. This review mainly focused on the benefits of probiotics/prebiotics on the GI microbial ecosystem in ruminants, which is deeply involved in nutrition and health for the animal.

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Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed.

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In the present study, we evaluated the viability of non-enveloped viruses, minute virus of mice (MVM) and coxsackievirus B4 (CVB4), and enveloped-viruses, influenza A virus (H1N1) and herpes simplex virus type 1 (HSV-1), on surfaces. We also investigated the impact of the initial concentration of proteins and sodium chloride on the persistence of infectious CVB4 on surfaces. Viral suspensions (>10^4.5 TCID₅₀) were applied to petri dish lids and dried under the air flow of a biosafety cabinet. The recovered viral preparations were titered on appropriate cell lines. Enveloped viruses persisted for less than 5 days while CVB4 and MVM persisted for weeks. However, repetitive cycles of drying and resuspension had a stronger virucidal effect on CVB4 than on H1N1 and HSV-1. These repetitive cycles had no effect on the infectious titer of MVM. When exposed to drying, the initial concentrations of bovine serum albumin (from 0 to 90 mg mL⁻¹), fetal calf serum (from 0 to 100%), and sodium chloride (from 0 to 300 mg mL⁻¹) affected the viability of CVB4. CVB4 was more likely to be inactivated by drying in a protein-rich medium, whereas the impact of drying was reduced in the presence of sodium chloride. The results of the present study demonstrated that the resistance of viruses to drying, as suggested by iterative drying, was not due to the heterogeneity of viral subpopulations, but was influenced by media compositions and component concentrations, as illustrated in the model of CVB4.

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The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

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Resuscitation-promoting factor (Rpf) is a protein that has been found in a number of different Actinobacteria species and has been shown to promote the growth of active cells and resuscitate dormant (non-dividing) cells. We previously reported the biological activity of an Rpf protein in Tomitella biformata AHU 1821^T, an Actinobacteria isolated from a permafrost ice wedge. This protein is excreted outside the cell; however, few studies have investigated its contribution in environmental samples to the growth or resuscitation of bacteria other than the original host. Therefore, the aim of the present study was to determine whether Rpf from T. biformata impacted the cultivation of other bacteria from the permafrost ice wedge from which it was originally isolated. All experiments used recombinant Rpf proteins produced using a Rhodococcus erythropolis expression system. Dilutions of melted surface sterilized ice wedge samples mixed with different doses of the purified recombinant Rpf (rRpf) protein indicated that the highest concentration tested, 1250 pM, had a significantly (p <0.05) higher number of CFUs on agar plates after 8 d, approximately 14-fold higher than that on control plates without rRpf. 16S rRNA gene sequences revealed that all the colonies on plates were mainly related to Brevibacterium antiquum strain VKM Ac-2118 (AY243344), with 98–99% sequence identity. This species is also a member of the phylum Actinobacteria and was originally isolated from Siberian permafrost sediments. The results of the present study demonstrated that rRpf not only promoted the growth of T. biformata from which it was isolated, but also enhanced colony formation by another Actinobacteria in an environmental sample.

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We herein analyzed the diversity of microbes involved in anaerobic sulfur oxidation in an upflow anaerobic sludge blanket (UASB) reactor used for treating municipal sewage under low-temperature conditions. Anaerobic sulfur oxidation occurred in the absence of oxygen, with nitrite and nitrate as electron acceptors; however, reactor performance parameters demonstrated that anaerobic conditions were maintained. In order to gain insights into the underlying basis of anaerobic sulfur oxidation, the microbial diversity that exists in the UASB sludge was analyzed comprehensively to determine their identities and contribution to sulfur oxidation. Sludge samples were collected from the UASB reactor over a period of 2 years and used for bacterial 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and next-generation sequencing analyses. T-RFLP and sequencing results both showed that microbial community patterns changed markedly from day 537 onwards. Bacteria belonging to the genus Desulforhabdus within the phylum Proteobacteria and uncultured bacteria within the phylum Fusobacteria were the main groups observed during the period of anaerobic sulfur oxidation. Their abundance correlated with temperature, suggesting that these bacterial groups played roles in anaerobic sulfur oxidation in UASB reactors.

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Dehalococcoides spp. are currently the only organisms known to completely reduce cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC) to non-toxic ethene. However, the activation of fermenting bacteria that generate acetate, hydrogen, and CO₂ is considered necessary to enhance the dechlorination activity of Dehalococcoides and enable the complete dechlorination of chloroethenes. In the present study, we stimulated chloroethene-contaminated groundwater by injecting different nutrients prepared from yeast extract or polylactate ester using a semicontinuous culture system. We then evaluated changes in the bacterial community structure and their relationship with dechlorination activity during the biostimulation. The populations of Dehalococcoides and the phyla Bacteroidetes, Firmicutes, and Spirochaetes increased in the yeast extract-amended cultures and chloroethenes were completely dechlorinated. However, the phylum Proteobacteria was dominant in polylactate ester-amended cultures, in which almost no cis-DCE and VC were dechlorinated. These results provide fundamental information regarding possible interactions among bacterial community members involved in the dechlorination process and support the design of successful biostimulation strategies.

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The lichen genus Peltigera has been mainly revised in the Northern Hemisphere, with most species being recorded in Europe and North America. This study assessed the phylogenetic diversity of the mycobionts and cyanobionts of Peltigera cyanolichens collected in Southern Chile and Antarctica, areas in which lichens are extremely diverse but poorly studied. The operational taxonomic units (OTUs) of each symbiont were defined by analyzing the genetic diversity of the LSU and SSU rDNA of the mycobionts and cyanobionts, respectively, and a phylogenetic approach was used to relate these OTUs with sequences previously reported for Peltigera and Nostoc. Among the 186 samples collected, 8 Peltigera and 15 Nostoc OTUs were recognized, corresponding to sections Peltigera, Horizontales, and Polydactylon, in the case of the mycobionts, and to the Nostoc clade II, in the case of the cyanobionts. Since some of the OTUs recognized in this study had not previously been described in these areas, our results suggest that the diversity of Peltigera reported to date in the regions studied using traditional morphological surveys has underestimated the true diversity present; therefore, further explorations of these areas are recommended.

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Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication.

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Bacteria often thrive in natural environments through a sessile mode of growth, known as the biofilm. Biofilms are well-structured communities and their formation is tightly regulated. However, the mechanisms by which interspecies interactions alter the formation of biofilms have not yet been elucidated in detail. We herein demonstrated that a quorum-sensing signal in Pseudomonas aeruginosa (the Pseudomonas quinolone signal; PQS) inhibited biofilm formation by Streptococcus mutans. Although the PQS did not affect cell growth, biofilm formation was markedly inhibited. Our results revealed a unique role for this multifunctional PQS and also indicated its application in the development of prophylactic agents against caries-causing S. mutans.

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Phosphate release from sediments hampers the remediation of aquatic systems from a eutrophic state. Microbial phosphatases in sediments release phosphorus during organic matter degradation. Despite the important role of phosphatase-expressing bacteria, the identity of these bacteria in sediments is largely unknown. We herein presented a culture-independent method to phylogenetically characterize phosphatase-expressing bacteria in sediments. We labeled whole-cell extracts of Baltic Sea sediments with an artificial phosphatase substrate and sorted phosphatase-expressing cells with a flow cytometer. Their phylogenetic affiliation was determined by Denaturing Gradient Gel Electrophoresis. The phosphatase-expressing bacterial community coarsely reflected the whole-cell bacterial community, with a similar dominance of Alphaproteobacteria.

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Fungi grow under humid conditions and are, therefore, prone to biofilm infections. A 16S rRNA fingerprint analysis was performed on 49 sporocarps of Basidiomycotina in order to determine whether they are able to control these biofilms. Ninety-five bacterial phylotypes, comprising 4 phyla and 10 families, were identified. While ectomycorrhizal fungi harbored the highest bacterial diversity, saprophytic fungi showed little or no association with bacteria. Seven fungal species were screened for antimicrobial and antibiofilm activities. Biofilm formation and bacterial growth was inhibited by extracts obtained from saprophytic fungi, which confirmed the hypothesis that many fungi modulate biofilm colonization on their sporocarps.

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Metagenomic studies have revealed the unexplored diversity of the environmental virosphere. However, most studies are biased towards specific types of viral genomes due to the absence of universal methods to access all viral genome types. In the present study, we established a novel system to efficiently separate single- and double-stranded DNA/RNA viral genomes using hydroxyapatite and cellulose chromatography. This method will allow us to quantitatively and simultaneously access four types of viral genomes and will provide important clues to further understand previously unexplored environmental viral populations and obtain potentially unbiased libraries from environmental viral communities.

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