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Mangrove sediments host a diverse array of microbial populations and are characterized by high heterogeneity along their vertical depths. However, the genetic diversity within these populations is largely unknown, hindering our understanding of their adaptive evolution across the sediment depths. To elucidate their genetic diversity, we utilized metagenome sequencing to identify 16 high‐frequency microbial populations comprised of two archaea and 14 bacteria from mangrove sediment cores (0–100 cm, with 10 depths) in Qi'ao Island, China. Our analysis of the genome‐wide genetic variation revealed extensive nucleotide diversity in the microbial populations. The genes involved in the transport and the energy metabolism displayed a high nucleotide diversity (HND; 0.0045–0.0195; an indicator of shared minor alleles with the microbial populations). By tracking the processes of homologous recombination, we found that each microbial population was subjected to different purification selection levels at different depths (44.12% genes). This selection resulted in significant differences in synonymous/non‐synonymous mutation ratio between 0–20 and 20–100 cm layers, indicating the adaptive evolutionary process of microbial populations. Furthermore, our assessment of differentiation in the allele frequencies between these two layers showed that the functional genes involved in the metabolic processes of amino acids or cofactors were highly differential in more than half of them. Together, we showed that the nucleotide diversity of microbial populations was shaped by homologous recombination and gene‐specific selection, finally resulting in the stratified differentiation occurring between 0–20 and 20–100 cm. These results enhance our cognition of the microbial adaptation mechanisms to vertical environmental changes during the sedimentation process of coastal blue carbon ecosystems. [ABSTRACT FROM AUTHOR]

Objectives Animals Studied Methods Results Conclusions To determine normal ocular parameters of the MacQueen's bustard (Chlamydotis macqueenii) and describe ophthalmic lesions in a captive bred population.Captive breeding population of 257 Macqueen's bustards.All birds were screened for ocular abnormalities using direct ophthalmoscopy. Abnormalities were photographed. Normative values for Schirmer tear test‐1 (STT‐1), applanation tonometry, aerobic and anaerobic bacterial culture, fungal culture, and transcorneal ocular ultrasonography were derived from multiple cohorts of clinically normal adult birds. Five birds with ocular pathology also underwent transcorneal ultrasonography. Statistical comparisons for normative values between OD and OS, and males and females were made using a paired t‐test or Mann–Whitney U‐test, with a significance level of p < .05.Mean tear production based on Schirmer tear test 1 (STT‐1) was 10.16 ± 4.61 mm/min (3–21 mm/min). Mean intraocular pressure (IOP) was 12.42 ± 4.94 mm Hg (5–26 mm Hg). Staphylococcus species were the most isolated bacteria from the conjunctival surfaces of normal birds (85%). Significant differences were found in transcorneal ultrasonographic measurements between males and females for axial globe length (p = .032), vitreous body depth (p = .049) and lens thickness (p = .0428). Corneal fibrosis was the most observed ocular abnormality amongst eyes with pathological changes (39%).Schirmer tear testing, tonometry and transcorneal ultrasound can easily be utilized in MacQueen's bustards and provide reproducible results. Normal parameters for these tests were determined, and common pathological ocular changes were described in this species. [ABSTRACT FROM AUTHOR]

Interstitial water or pore water occupies the space between soil particles and provides "hotspots" and "fluvial networks" for microbial activities in floodplain soil. However, to date, we know very little about the microorganisms living in pore water and how they respond to environmental changes. This study aimed to understand microbial distribution and assemblage in riparian pore waters, and how they respond to water chemistry and redox gradients associated with hydrological processes.We analysed the annual changes of porewater microbial communities from the east and west banks of the White Clay Creek, a site at the Christina River Basin – Critical Zone Observatory, Pennsylvania, USA. Microbial abundances were quantified by epifluorescence microscopy and detailed community structures were characterised by high‐throughput sequencing. Water chemistry and redox gradients were also monitored and recorded, and their interactions with porewater microbiomes were analysed using correlations and multivariate analyses.Abundance of microbial cells increased during summer and late autumn. Wetland porewater microbiomes mainly contained Acidobacteria, Bacteroidetes, Nitrospirae and Proteobacteria, and microbiome structures were easily distinguishable from those in the underlying hyporheic gravel layer. Seasonal dynamics of bacterial community structure in the east and west wetlands were distinct, responding to floodplain topography and associated hydrological/geochemical processes. Iron (Fe)‐cycling bacteria (mainly Gallionellaceae and Rhodoferax spp.) dominated the porewater microbiome, and their relative abundance was significantly higher in the east than the west wetland. Furthermore, Fe‐oxidising bacteria (Gallionellaceae) were negatively correlated with Fe‐reducing bacteria (Rhodoferax spp.) at the east wetland.Microbial abundances (cell density) in pore waters showed similar seasonal patterns across stream banks, but microbial community structure did not. Microbiome assembly in pore water is correlated with water chemistry and redox gradients primarily associated with local hydrological processes.As a consequence of their significance for carbon (C) mineralisation and Fe reduction at terrestrial–aquatic interfaces, microbiomes in riparian pore waters and associated microbial activity play an essential role in C and mineral dynamics. These findings will inform future studies of the response of freshwater ecosystems to hydrological dynamics influenced by global climate change. [ABSTRACT FROM AUTHOR]

BACKGROUND: The objective was to determine how molasses and Lactobacillus plantarum affect chemical composition, fermentation quality, aerobic stability, and the microbial community of an ensiled mixture of amaranth (Amaranthus hypochondriaus, AF) and rice straw. Treatments were control (C, no addition), L. plantarum (L; 2 × 105 cfu g−1 fresh weight), molasses (M; 40 g kg−1 fresh matter), and their combination (LM). All treatments were ensiled for 1, 3, 5, 7, and 30 days. RESULTS: All additives improved fermentation quality with greater lactic acid (LA), acetic acid, and lower pH than C silage over the ensiling period. The LM silage combination optimized fermentability, manifested as greater LA contents and a more rapid pH reduction during the first 7 days of ensiling than L or M silages. After 30 days of ensiling, inoculant L. plantarum increased Lactobacillus abundance and reduced bacterial diversity and Enterobacteriaceae abundance compared with silage treated with molasses. Molasses addition reduced the relative concentration of structural carbohydrates (neutral and acid detergent fiber, and hemicellulose) after 30 days of ensiling. Finally, there was spoilage after 2 days and 4 days of aerobic exposure in C and LM silages respectively, whereas L silage had not spoiled after 4 days. CONCLUSIONS: Although the combination of L. plantarum and molasses further optimized fermentation characteristics, L silage had better aerobic stability. © 2021 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The nutritive value, fermentation profile, microbial population, and effluent and gases losses of sweet potato vine silages, with and without microbial inoculant, were evaluated. The experiment was conducted in a 5 × 2 factorial arrangement, with five sweet potato genotypes (BD‐08, BD‐23, BD‐25, BD‐31TO and BD‐43) and presence/absence of microbial inoculant (Sil‐All® 4 × 4), in a randomized blocks design, with three replicates. After 48 hr of wilting in field, the vines were chopped, inoculated with microbial inoculant and ensiled in 10‐L plastic buckets. The genotype × microbial inoculant interaction was significant (p <.05) only for in vitro dry matter digestibility (IVDMD), whose coefficients ranged from 64.2% to 74.2%. The genotype affected significantly (p <.05) the pH, dry matter and acid detergent fiber contents, and lactic and acetic acid concentrations of the silages. The inoculant affected significantly (p <.05) the pH, ammonia nitrogen, and lactic acid contents, and gases losses. We concluded that all genotypes of sweet potato produced good quality silages. Microbial inoculant reduced pH, ammonia nitrogen concentration and gases losses, and increased lactic acid content of silages. The IVDMD of silages made from BD‐25 and BD‐31TO genotypes was improved with microbial inoculant. [ABSTRACT FROM AUTHOR]

BACKGROUND The aim of the current research was to clarify the impacts of the ensiling of whole‐plant hybrid pennisetum with natamycin and Lactobacillus plantarum on fermentation characteristics and the meta‐genomic microbial community at low temperatures. RESULTS: During the ensiling process, lactic acid (LA) and lactic acid bacteria (LAB) significantly (P < 0.05) increased and acetic acid (AA), water‐soluble carbohydrate (WSC), ammonia total nitrogen (NH3‐N), and yeast significantly (P < 0.05) reduced in treatments as compared to controls. Different treatments and different ensiling days led to variations in the bacterial community at family and genus levels. The family Lactobacillaceae and genera Lactobacillus and Pediococcus are dominant communities in treatment silage. The family and genus levels bacterial ecology and fermentation quality were analyzed by principal component analysis (PCA). The PCO1, and PCO2 can be explained by 10.81% and 72.14% of the whole variance regularly, similarly in PCO1 and PCO2 can be explained 24.23% and 52.06% regularly. The core bacterial micro‐biome operational taxonomic unit (OTU) numbers increased in treatments, as compared to controls, on different hybrid pennisetum ensiling days. CONCLUSIONS: The inoculation of L. plantarum alone and combined with natamycin influenced the fermentation quality and reduced undesirable microorganisms during the fermentation of hybrid pennisetum silage. Natamycin alone did not significantly enhance the concentration of organic acid but numerically enhanced in treatments group as compared to control. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

BACKGROUND: Yeast products showed beneficial effects with respect to stabilizing ruminal pH, stimulating ruminal fermentation and improving production efficiency. Batch cultures were conducted to evaluate the effects of yeast products on gas production (GP), dry matter disappearance (DMD) and fermentation characteristics of high‐forage substrate. The study was a two media pH (5.8 and 6.5) × five yeasts (three live yeasts, LY: LY1, LY2, LY3; two yeast derivatives, YD: YD4, YD5) × four dosages factorial arrangement, with monensin (Mon) assigned as a positive control. RESULTS: Greater (P < 0.01) GP, DMD, volatile fatty acid (VFA) concentration, ratio of acetate to propionate (A:P) and copy numbers of Fibrobacter succinogenes and Ruminococcus flavefaciens were observed at pH 6.5 than at pH 5.8. The GP kinetics, DMD, VFA concentration, A:P and NH3‐N concentration differed (P < 0.05) among yeasts but varied with media pH or yeast dosages. Increasing doses of LY3 linearly increased DMD (P < 0.04) and VFA concentration (P < 0.001) at media pH 5.8. The DMD linearly (P < 0.02) increased with increased addition of YD4 (pH 6.5) and YD5 (pH 5.8) and the ratio of A:P linearly decreased (P < 0.01) with the addition of YD4 or YD5 at pH 5.8. Overall greater (P < 0.05) GP, A:P (pH 5.8) and DMD (pH 6.5) were observed with yeast products than with Mon. CONCLUSION: LY3 appeared to be an interesting candidate for improving rumen digestibility and fermentation efficiency, particularly at low media pH. YD4 or YD5 improved fermentation efficiency and can be potentially fed as an alternative to Mon. © 2019 Her Majesty the Queen in Right of Canada Journal of the Science of Food and Agriculture © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

BACKGROUND: Anaerobic digestion (AD) could be designed as a source of volatile fatty acids (VFAs). However, acidogenesis optimization for novel substrates such as Chlorella vulgaris biomass needs to be investigated considering parameters such as temperature (T), organic loading rate (OLR), hydraulic retention time (HRT) and the adaptation of the sludge to temperature and substrate. RESULTS: The best organic matter conversion into VFAs (CODVFA/CODin; COD, chemical oxygen demand) was achieved with HRT = 8 d, adapted anaerobic sludge (AAS) and OLR = 1.5 gCOD L−1 d−1 (CODVFA/CODin = 39.8 ± 1.0% and productivity VFA = 0.5 ± 0.1 g L−1 d−1). Acetic and butyric acids represented 50% of the total VFAs. The microbiota related to acidogenesis and acetogenesis (Firmicutes 55% of the operational taxonomic units in R5) and the low archaeal population resulted in VFA accumulation at 25 °C. CONCLUSIONS: The use of low HRT and temperatures promoted VFAs production especially when AAS was employed. Microbial communities were strikingly different to the ones often found in AD targeted at biogas production. The relevance of the Firmicutes phylum (≤55% in R3 and R5) and euryarchaeota absence at 25 °C contributed to VFA accumulation. The use of AAS reported an increase in Actinobacteria species. © 2019 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Abstract: Silage was made from the dominant native grasses growing on the Inner Mongolian Plateau, including Baical needlegrass (Stipa baicalensis), China leymus (Leymus chinensis), Scabrous hideseedgrass (Cleistogenes squarrosa), Ruthenia medic (Melissilus ruthenicus) and Slenderleaf pulsatilla (Pulsatilla turczaninovii) and their microbial populations, chemical composition and silage fermentation were studied. Before ensiling, these grasses contained per g of fresh matter (FM) 105 lactic acid bacteria (LAB) cell‐forming units (cfu), 107 aerobic bacteria, 103–105 coliform bacteria, yeasts and molds. The LAB counts increased rapidly after 2 days of fermentation and remained dominant during the fermentation process. After 7 days of ensiling, the coliform bacteria and molds were below detectable levels in all silages. The crude protein (CP) of these grasses ranged from 8.93 to 14.95% of dry matter (DM), and the neutral detergent fiber (NDF) comprised 58.29–70.05% of DM. Crude protein content of Ruthenia medic was higher and the NDF and acid detergent fiber (ADF) contents of Slenderleaf pulsatilla were lower than those of the other grasses. During ensiling, the organic matter, CP, ether extract, NDF and ADF contents in each kind of silage did not differ significantly (P > 0.05). During the progression of ensiling, the lactic acid and acetic acid contents increased in all silages, while the pH decreased. At day 30, all silages had similar fermentation patterns; more than 0.58% FM lactic acid was produced and the pH was reduced below 4.44. The results suggest that the native grasses can be used to prepare good quality silages. [ABSTRACT FROM AUTHOR]

Compost is beneficial for agriculture fields in many ways such as soil conditioner, fertilizer, and natural pesticide and above all it helps to manage organic wastes and adds vital humic acids to soil. Four indigenous composts prepared from readily available organic wastes viz. vermicompost, banana, NADEP, and Calotropis were used in the present investigation for growth and disease suppression in mung beans. The composts were amended with Trichoderma viride in the concentration of 0.1 and 0.2% to determine their influence on length and weight of roots and shoots, disease incidence, soil moisture, and soil microflora in plants. The best results were observed in the treatment with T. viride (0.2%), followed by T. viride (0.1%) in vermicompost, while the treatment T. viride (0.1%) with Calotropis compost showed little growth and suppression of disease. All composts enhanced the soil moisture content and microbial populations in amended soil resulting in the reduction of disease incidence. Among T. viride enriched composts, the counts of fungi, bacteria, and actinomycetes were higher in the vermicompost and banana compost-amended soils. Thus, preparing these composts from readily available organic wastes and amending soil with T. viride enriched composts hold a great promise for improving soil fertility and suppressing the soil-borne plant pathogens for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Four, rumen fistulated swamp buffalo bulls were used to study microbial populations in the rumen when supplemented with coconut oil and mangosteen peel. Animals were randomly assigned to a 4 × 4 Latin square design. Four treatments were un-supplemented (Control), supplementation with coconut oil at 50 g/kg (CO5), supplementation with mangosteen peel at 30 g/kg (MP3) and supplementation with CO5 and MP3 (COM), of total DM intake. Animals received concentrate at 10 g/kg of BW, and rice straw was given ad libitum. Abundance of total bacteria was increased by CO5 supplementation, whereas populations of protozoa and Fibrobacter succinogenes were reduced by CO5 and COM supplementation. Dietary supplementation did not affect methanogen, Ruminococcus flavefaciens or Ruminococcus albus abundances. Dietary treatments changed denaturing gradient gel electrophoresis (DGGE) band patterns of methanogens and protozoa when compared with the control group, especially when supplemented with MP3. Supplementation of COM resulted in the greatest difference in pattern of DGGE bands for total bacteria compared with the control. Coconut oil and mangosteen peel supplementation resulted in changing of rumen microbial abundances and communities; however, combination of them could be more benefit to improve rumen fermentation of swamp buffalo fed on rice straw. [ABSTRACT FROM AUTHOR]

Summary: Coffee pulp is the main solid residue from the wet processing of coffee berries. Recent stringent measures by Pollution Control authorities, made it mandatory to treat all the solid and liquid waste emanating from the coffee farms. A study was conducted to evaluate the efficiency of an exotic ( Eudrilus eugeniae) and a native earthworm ( Perionyx ceylanesis) from coffee farm for decomposition of coffee pulp into valuable vermicompost. Exotic earthworms were found to degrade the coffee pulp faster (112 days) as compared to the native worms (165 days) and the vermicomposting efficiency (77.9%) and vermicompost yield (389 kg) were found to significantly higher with native worms. The multiplication rate of earthworms (280%) and worm yield (3.78 kg) recorded significantly higher with the exotic earthworms. The percentage of nitrogen, phosphorous, potassium, calcium and magnesium in vermicompost was found to increase while C:N ratio, pH and total organic carbon declined as a function of the vermicomposting. Vermicompost and vermicasts from native earthworms recorded significantly higher functional microbial group's population as compared to the exotic worms. The study reveals that coffee pulp can be very well used as substrate for vermicomposting using exotic ( Eudrilus eugeniae) and native earthworm ( Perionyx ceylanesis). [ABSTRACT FROM AUTHOR]

BACKGROUND: Douchi is a traditional Chinese soybean food which has been consumed for thousands years as an important protein source and flavouring ingredient. Studies have rarely been carried out to investigate its microbial composition and these are urgently required for the commercial labels and safety considerations. RESULTS: Microbial counts were statistically significant different among Douchi samples. Although the maximum diversity indexes of bacterial, bacillus and fungal polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) patterns were only 79%, 70% and 64%, some microorganisms, e.g. Bacillus subtilis, Bacillus amyloliquefaciens, Pseudomonas sp., Saccharomyces cerevisiae and Pichia farinose, were found to share dominant positions in most Douchi samples. In addition, some pathogens, e.g. Staphylococcus saprophyticus, Pantoea sp., Staphylococcus sciuri, Enterobacter sp. and Staphylococcus sp., were also identified. CONCLUSION: The PCR-DGGE technique was used for the first time as an effective method to assess the microbial communities in different Chinese Douchi samples. This information may be useful in improving the product quality, reformatting production methods, extending shelf life and scaling up the fermentation process. Copyright © 2012 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

We observed the effects of a commercial microbiological additive (MA) on the beef manure composting process and investigated the changes in its physical and chemical components and microbial populations in the composting process. When beef manure compost was inoculated with the MA, its temperature rapidly increased at the beginning of the process, and after the first turning, the ammonia emission from the compost pile and nitrate production decreased quicker than that in the composting process without the MA. During the composting process, the manure inoculated with MA showed a larger numbers of mesophilic and thermophilic aerobes, and a smaller number of thermophilic anaerobes than in the process without the MA. These results suggested that mesophilic aerobes increased in number and metabolized ammonia by assimilation rather than nitrification to accelerate the temperature elevation in the composting process with the MA. [ABSTRACT FROM AUTHOR]

Tsunami, the natural disaster, which occurred on December 26, 2004 in the Indian Ocean, caused severe damage to mankind in the coastal areas. Total loss of life and economic loss because of this disaster have been estimated by various agencies but its effect on microbial density has not been probed. With our previous results on microbial populations in four locations of the Chennai coast of the Bay of Bengal, India in the pre-tsunami period, the change in microbial populations was studied after the tsunami at regular intervals in the same locations. Coastal sediment and seawater samples were collected from four different locations after 5–10 h and thereafter at intervals of every 7 days up to 28 days post-tsunami. Bacteria, fungi and actinomycetes were isolated from the marine samples by serial dilution on respective media. Before the tsunami, the bacterial population was higher in seawater samples than the sediments, whereas fungi and actinomycetes were recorded only in the sediments. The microbial population remarkably increased 5–10 h post-tsunami in all the marine samples irrespective of the location. However, it slowly declined in the subsequent days and became similar to that of the population recorded before the tsunami. The population of gram-positive bacteria increased whereas the gram-negative bacterial population decreased after the tsunami. Further, populations of pathogenic bacteria such as coliform and vibrios did not increase after the tsunami. It has been observed that the increase in populations of bacteria and actinomycetes even after 28 days of tsunami may be due to the introduction of foreign microorganisms that developed the ability to survive in the extreme environment by exhibiting special characteristics such as pigmentation and production of exopolysaccharides. [ABSTRACT FROM AUTHOR]

SummaryAn increase in concentration of atmospheric CO2 is one major factor influencing global climate change. Among the consequences of such an increase is the stimulation of plant growth and productivity. Below-ground microbial processes are also likely to be affected indirectly by rising atmospheric CO2 levels, through increased root growth and rhizodeposition rates. Because changes in microbial community composition might have an impact on symbiotic interactions with plants, the response of root nodule symbionts to elevated atmospheric CO2 was investigated. In this study we determined the genetic structure of 120 Rhizobium leguminosarum bv. trifolii isolates from white clover plants exposed to ambient (350 μmol mol-1) or elevated (600 μmol mol-1) atmospheric CO2 concentrations in the Swiss FACE (Free-Air-Carbon-Dioxide-Enrichment) facility. Polymerase Chain Reaction (PCR) fingerprinting of genomic DNA showed that the isolates from plants grown under elevated CO2 were genetically different from those isolates obtained from plants grown under ambient conditions. Moreover, there was a 17% increase in nodule occupancy under conditions of elevated atmospheric CO2 when strains of R. leguminosarum bv. trifolii isolated from plots exposed to CO2 enrichment were evaluated for their ability to compete for nodulation with those strains isolated from ambient conditions. These results indicate that a shift in the community composition of R. leguminosarum bv. trifolii occurred as a result of an increased atmospheric CO2 concentration, and that elevated atmospheric CO2 affects the competitive ability of root nodule symbionts, most likely leading to a selection of these particular strains to nodulate white clover. [ABSTRACT FROM AUTHOR]

Maize (Zea mays L. cv. Tau) plants were grown in a calcareous soil for six weeks in pots having separate compartments for growth of roots and vesicular-arbuscular (VA) mycorrhizal fungal hyphae. Soil was sterilized and either left non-inoculated (sterile treatment), or was inoculated with rhizosphere micro-organisms only (MO-VA) or with rhizosphere micro-organisms together with a VA mycorrhizal fungus [Glomus mosseae (Nicol. & Gerd.) Gerdemann & Trappe (MO + VA)]. Concentrations of Mn in roots and shoots, as well as exchangeable Mn in rhizosphere soil, decreased in the order MO - VA > MO + VA > sterile treatment. In all treatments, the concentration of exchangeable Mn was lower in the rhizosphere soil (0-5 mm distance from the root surface) than in the bulk soil (5-15 or 15-25 mm distance from the root surface). In the rhizosphere soil, the total microbial population was similar in mycorrhizal (MO + VA) and non-mycorrhizal (MO - VA) treatments, but the proportion of Fe- or Mn-reducers was 20- to 30-fold higher in the non-mycorrhizal treatment, suggesting substantial qualitative changes in rhizosphere microbial populations upon root infection with the mycorrhizal fungi. The Mn+IV-reducing potential (net balance between reduction and oxidation) in the rhizosphere soil was also distinctly lower in mycorrhizal treatment compared to non-mycorrhizal treatment. In the sterile treatment, low Mn+IV-reducing potential and correspondingly low concentration of exchangeable Mn in soil, compared to the other treatments, indicates the importance of micro-organisms in Mn reduction in soil and acquisition of Mn by plants. Therefore, the lower Mn concentrations in mycorrhizal plants are most probably caused by a shift in composition and activity of rhizosphere micro-organisms. As a side effect of the treatments, improved soil aggregation, as indicated by soil adhering to the nylon net (facing hyphal compartments) after plant harvest, occurred in non-mycorrhizal and sterile treatments but not in the mycorrhizal treatment. [ABSTRACT FROM AUTHOR]

Microbial populations in probiotic supplements in China were investigated using the plate count method and PCR- DGGE technique. Our results indicated that total viable cells in most probiotic products could meet the minimum requirement of the Chinese National Standards (106 CFU/ mL); however, total viable cell counts of the species detected in the probiotic products did not correspond with the cell number given in the label. [ABSTRACT FROM AUTHOR]