Abundance Of Microbial Groups Research Articles

무기질비료의 장기연용이 토양생물 및 먹이연쇄에 미치는 영향

BACKGROUND: This study aimed to evaluate the combined effects of three components (NPK) of chemical fertilizers with basal application of compost on soil organisms.METHODS AND RESULTS: The soil was treated with five treatments continuously for 15 years: control, PK, NK, NP and NPK. The application of N increased plant growth or biomass, and enhanced organic matter content in the soils. Levels of microbial phospholipid fatty acids (PLFAs) in the soils did not show marked differences among the soils treated with different treatments. However, the principal component analysis showed the changes in the structure of the microbial community in the soil, depending on treatments added. Nitrogen application caused a decrease of pH and an increase of EC in the soils, and these environmental stresses appeared to offset the promoting effect of increased organic matter content on microbial abundance. The abundance of bacterivorous nematodes was the highest in the soils after treating NPK; however, the abundance of fungivorous nematodes was unaffected. There was no significant correlation between the abundances of microbial groups and their feeders. Organic matter content was significantly correlated with the abundance of nematodes in the soils.CONCLUSION: Our results showed that chemical fertilizers affect the soil food chains through both biotic and abiotic factors, and a trophic cascade in the soils may not occur in response to long-term fertilization.

Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils.

Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our mechanistic understanding of biogeochemical cycles.

Plant-specific effects of sunn hemp (Crotalaria juncea) and sudex (Sorghum bicolor × Sorghum bicolor var. sudanense) on the abundance and composition of soil microbial community

We investigated the effect of sunn hemp (leguminous) and sudex (non-leguminous) on the abundance and composition of microbial community in soil with a low nutrient content for two years. Abundance of microbial groups was determined by phospholipid fatty acid (PLFA) analysis. Pyrosequencing analysis was used to compare the composition of bacterial communities in the rhizosphere with that in the bulk soil of the unplanted control. The concentration of microbial PLFA increased during cultivation period and decreased after incorporation of plant residues, which implies that the responses depended on living plants. Overall, the bacterial PLFA concentration was lower with sunn hemp than sudex, despite the above-ground biomass was about five times greater with the former than with the latter crop. This indicates that the increase in bacterial PLFA with sudex is plant-specific. Pyrosequencing analysis revealed that the abundance of Arthrobacter, Bacillus, and Sphingomonas were the highest in the bulk soil and decreased in the rhizospheres of the cover plants. The proportions of Gaiella and the nitrogen fixing bacteria Mesorhizobium increased with sunn hemp, while those of cyanobacteria, including Calothrix, Leptolyngbya, and Nostoc, increased greatly with sudex. Our results indicated that the high level of bacterial PLFA with sudex could be primarily explained by the colonization of cyanobacteria. We show that the impacts of cover plants on the abundance and composition of the microbial communities depend more on the plant species than on the aboveground plant biomass, both during growth and incorporation stages. Our results also suggest that non-leguminous as well as leguminous plants harbor beneficial microbes such as nitrogen-fixing bacteria to cope with nutrient-poor environments.

Water availability and abundance of microbial groups are key determinants of greenhouse gas fluxes in a dryland forest ecosystem

Forests are considered key biomes that could contribute to minimising global warming as they sequester carbon (C) and contribute to mitigate emissions of the potent greenhouse gases (GHG) including nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2). Management practices are prevalent in forestry, particularly in dryland ecosystems, known to be water and nitrogen (N) limited. Irrigation and fertilisation are thus routinely applied to increase the yield of forest products. However, the contribution of forest management practices to current GHG budgets and consequently to soil net global warming potential (GWP) is still largely unaccounted for, particularly in dryland ecosystems. We quantified the long-term effect (six years) of irrigation and fertilisation and the impact of land-use change, from grassland to a Eucalyptus plantation on N2O, CH4 and CO2 emissions and soil net GWP, within a dryland ecosystem. To identify biotic and abiotic drivers of GHG emissions, we explored the relationship of N2O, CH4 and CO2 fluxes with soil abiotic characteristics and abundance of ammonia-oxidizers, N2O-reducing bacteria, methanotrophs and total soil bacteria. Our results show that GHG emissions, particularly N2O and CO2 are constrained by water availability and both N2O and CH4 are constrained by N availability in the soil. We also provide evidence of functional microbial groups being key players in driving GHG emissions. Our findings illustrate that GHG emission budgets can be affected by forest management practices and provide a better mechanistic understanding for future mitigation options.

Detection and Enumeration of Lactic Acid Bacteria, Acetic Acid Bacteria and Yeast in Kefir Grain and Milk Using Quantitative Real‐Time PCR

AbstractKefir is a unique fermented dairy product that is produced by a mixture of lactic acid bacteria, acetic acid bacteria and yeast. In this study, a culture‐independent quantitative real‐time polymerase chain reaction (PCR) technique was used to enumerate lactic acid bacteria, acetic acid bacteria and yeast in kefir grain and kefir milk using group‐specific primers. The most abundant microbial groups were lactic acid bacteria and acetic acid bacteria, followed by yeast (P < 0.05) in both kefir grain and kefir milk. The most leading genera of lactic acid bacteria and yeast were Lactobacillus/Lactococcus (P < 0.05) and Candida, respectively. All microbial groups were present in lower numbers in kefir milk than in kefir grain (P < 0.05), except for Enterococcus and Saccharomyces groups. This is the first report to characterize the number of specific microbial populations in kefir grain and kefir milk using quantitative real‐time PCR. In conclusion, we successfully established the methods for the quantification of microorganisms in kefir grain and kefir milk using group‐specific quantitative real‐time PCR and provided quantitative microbiological information for quality control of kefir.Practical ApplicationsThis report describes the enumerative methods of microorganisms in the kefir grain and kefir milk using group‐specific quantitative real‐time PCR assay. It could facilitate the microbiological quality control of kefir‐fermented milk and grain and can be used in further studies to understand the fermentation process of kefir milk. In addition, the results provide basic information on the number of lactic acid bacteria, acetic acid bacteria and yeast in kefir grain and kefir milk.

Effects of short-term conservation management practices on soil organic carbon fractions and microbial community composition under a rice-wheat rotation system

The objective of this study was to investigate the effects of short-term (less than 2 years) conservation managements [no-tillage (NT) and crop residue returning] on top soil (0–5 cm) microbial community composition and soil organic C (SOC) fractions under a rice-wheat rotation at Junchuan town of Hubei Province, China. Treatments were established following a split-plot design of a randomized complete block with tillage practices [conventional tillage (CT) and NT] as the main plot and residue returning level [no residue returning (0) and all residues returned to fields from the preceding crop (S, 2,146 kg C ha−1)] as the subplots. The four treatments were CT with or without residue returning (CT0 and CTS) and NT with or without residue returning (NT0 and NTS). The abundances of microbial groups [total FLFAs, fungal biomass, bacterial biomass, fungal biomass/bacterial biomass (F/B), monounsaturated fatty acids/saturated fatty acids (MUFA/STFA), and microbial stress] were determined by phospholipid fatty acid (PLFA) analysis of soil. The ratio of MUFA/STFA reflects aeration of soil and greater MUFA/STFA means better aeration condition of soil. Moreover, the microbial stress, the ratio of cy19:0 to 18:1ω7, was regarded as an indicator of physiological or nutritional stress of microbial community. PLFA profiles were dominated by the fatty acids iC15:0 (9.8 %), C16:0 (16.5 %), 10Me17:0 (9.9 %), and Cyc19:0 (8.3 %), together accounting for 44.6 % of the total PLFAs. Compared with CT, NT significantly increased microbial biomass C (MBC) by 20.0 % but did not affect concentrations of total organic C (TOC), dissolved organic C (DOC), easily oxidizable C (EOC), and SOC of aggregates. Residue returning significantly increased MBC by 18.3 % and SOC content of 2–1-mm aggregate by 9.4 %. NT significantly increased total PLFAs by 9.8 % and fungal biomass by 40.8 % but decreased MUFA/STFA by 15.5 %. Residue returning significantly enhanced total PLFAs, bacterial biomass, fungal biomass, F/B, and MUFA/STFA by 31.1, 36.0, 95.9, 42.5, and 58.8 %, respectively, but decreased microbial stress by 45.9 %. Multivariate analysis (redundancy analysis and partial correlation analysis) indicated that SOC of 2–1-mm aggregate was related to changes in the composition of soil microbial groups, suggesting that SOC of 2–1-mm aggregate was sensitive to changes in soil microbial community composition affected by short-term conservation management practices in our study.

Balanced Fertilization along with Farmyard Manures Enhances Abundance of Microbial Groups and Their Resistance and Resilience against Heat Stress in a Semi-arid Inceptisol

The impact of long-term (36-year) application of balanced fertilizers and farmyard manures (FYM) on the abundance of microbial groups (bacteria, fungi, actinomycetes, Pseudomonas, Azotobacter, ammonia-oxidizing bacteria) and their resistance and resilience against heat stress was investigated in a semi-arid Inceptisol at New Delhi, India. Surface soils from selected treatments [control, nitrogen (N), N and phosphorus (P), NP and potassium (K), NPK + FYM] under a maize crop were assessed immediately after sampling (0-day) and at 1, 14, 28, and 56 day(s) after heat stress (48 °C for 24 h). The heat stress significantly reduced the microbial groups by 20 to 80%. Recovery after stress was 60 to 100% within 56 days. Resistance and resilience of fungi and actinomycetes were greater than other groups of organisms. Ammonia-oxidizing bacteria (AOB) were found to be most sensitive with the lowest resistance index. Application of NPK + FYM was most effective in enhancing the resistance and resilience of soil microorganisms against heat stress.

Novel Cultivation-Based Approach To Understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from Sedimentary Ecosystems

The uncultured miscellaneous crenarchaeotic group (MCG) archaea comprise one of the most abundant microbial groups in the Earth's subsurface environment. However, very little information is available regarding the lifestyle, physiology, and factors controlling the distribution of members of this group. We established a novel method using both cultivation and molecular techniques, including a pre-PCR propidium monoazide treatment, to investigate viable members of the MCG in vitro. Enrichment cultures prepared from estuarine sediment were provided with one of a variety of carbon substrates or cultivation conditions and incubated for 3 weeks. Compared with the samples from time zero, there was an order-of-magnitude increase in the number of MCG 16S rRNA genes in almost all cultures, indicating that MCG archaea are amenable to in vitro cultivation. None of the tested substrates or conditions significantly stimulated growth of MCG archaea more than the basal medium alone; however, glycerol (0.02%) had a significantly inhibitory effect (P < 0.05). Diversity analysis of populations resulting from four culture treatments (basal medium, addition of amino acids, H2-CO2 as the gas phase, or initial aerobic conditions) revealed that the majority of viable MCG archaea were affiliated with the MCG-8 and MCG-4 clusters. There were no significant differences in MCG diversity between these treatments, also indicating that some members of MCG-4 and MCG-8 are tolerant of initially oxic conditions. The methods outlined here will be useful for further investigation of MCG archaea and comparison of substrates and cultivation conditions that influence their growth in vitro.

Microbial communities in Cerrado soils under native vegetation subjected to prescribed fire and under pasture

The objective of this work was to evaluate the effects of fire regimes and vegetation cover on the structure and dynamics of soil microbial communities, through phospholipid fatty acid (PLFA) analysis. Comparisons were made between native areas with different woody covers ("cerrado stricto sensu" and "campo sujo"), under different fire regimes, and a 20-year-old active palisadegrass pasture in the Central Plateau of Brazil. Microbial biomass was higher in the native plots than in the pasture, and the highest monthly values were observed during the rainy season in the native plots. No significant differences were observed between fire regimes or between communities from the two native vegetation types. However, the principal component (PC) analysis separated the microbial communities by vegetation cover (native x pasture) and season (wet x dry), accounting for 45.8% (PC1 and PC3) and 25.6% (PC2 and PC3), respectively, of the total PLFA variability. Changes in land cover and seasonal rainfall in Cerrado ecosystems have significant effects on the total density of soil microorganisms and on the abundance of microbial groups, especially Gram-negative and Gram-positive bacteria.

Soil microbial community dynamics and phenanthrene degradation as affected by rape oil application

The effects of rape oil application on soil microbial communities and phenanthrene degradation were characterized by examining phenanthrene concentrations, changes in microbial composition and incorporation of [ 13C] phenanthrene-derived carbon into phospholipid fatty acids (PLFAs). A Haplic Chernozem was incubated with and without rape oil in combination with and without phenanthrene over 60 days. High-performance liquid chromatography (HPLC) analysis showed a net reduction in extractable phenanthrene in the soils treated with rape oil but no net reduction in the soils without rape oil. Rape oil application increased the total PLFA content and changed microbial community composition predominantly due to growth of fungal groups and Gram-positive bacterial groups. Under rape oil and phenanthrene amendment all detected microbial groups grew until day 24 of incubation. The 13C PLFA profiles showed 13C enrichment for the PLFAs i14:0, 15:0, 18:0, 18:1ω5 and the fungal biomarker 18:2ω6,9 under rape oil application. Fungal PLFA growth was highest among detected all PLFAs, but its 13C incorporation was lower compared to the Gram-positive and Gram-negative bacteria PLFAs. Our results demonstrate the effect of rape oil application on the abundance of microbial groups in soil treated with phenanthrene and its impact on phenanthrene degradation.

Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight

Marine Crenarchaeota are among the most abundant microbial groups in the ocean, and although relatively little is currently known about their biogeochemical roles in marine ecosystems, recognition that Crenarchaeota posses ammonia monooxygenase (amoA) genes and may act as ammonia-oxidizing archaea (AOA) offers another means of probing the ecology of these microorganisms. Here we use a time series approach combining quantification of archaeal and bacterial ammonia oxidizers with bacterial community fingerprints and biogeochemistry, to explore the population and community ecology of nitrification. At multiple depths (150, 500 and 890 m) in the Southern California Bight sampled monthly from 2003 to 2006, AOA were enumerated via quantitative PCR of archaeal amoA and marine group 1 Crenarchaeota 16S rRNA genes. Based on amoA genes, AOA were highly variable in time - a consistent feature of marine Crenarchaeota- however, average values were similar at different depths and ranged from 2.20 to 2.76 x 10(4) amoA copies ml(-1). Archaeal amoA genes were correlated with Crenarchaeota 16S rRNA genes (r(2) = 0.79) and the slope of this relationship was 1.02, demonstrating that the majority of marine group 1 Crenarchaeota present over the dates and depths sampled possessed amoA. Two AOA clades were specifically quantified and compared with betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) amoA genes at 150 m; these AOA groups were found to strongly co-vary in time (r(2) = 0.70, P < 0.001) whereas AOA : beta-AOB ratios ranged from 13 to 5630. Increases in the AOA : beta-AOB ratio correlated with the accumulation of nitrite (r(2) = 0.87, P < 0.001), and may be indicative of differences in substrate affinities and activities leading to periodic decoupling between ammonia and nitrite oxidation. These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants.

Technological characterization of the natural lactic acid bacteria of artisanal Turkish White Pickled cheese

The aim of this study was to characterize the lactic acid bacteria (LAB) isolated from White Pickled cheeses produced with traditional methods; and to improve the quality of cheesemaking with a selection of bacterial cultures from artisanal White cheeses. LAB were isolated and identified from 30 White Pickled cheese samples collected from various cities in Turkey. Also, the numbers of several microbial groups (total aerobic mesophilic bacteria, LAB, enterococci, coliforms, moulds and yeasts) of cheese samples were enumerated. Lactobacilli, lactococci and enterococci were the most abundant microbial groups. The numbers of Enterococcus and Lactobacillus isolates were higher than those of the other LAB. Enterococcus faecalis (24.43%), Enterococcus faecium (17.61%) and Lactobacillus fermentum (19.88%) isolates were the most frequently isolated species. Lactococcus strains showed the highest acidifying activity, followed by Enterococcus and Lactobacillus strains. Proteolytic activity of Enterococcus faecalis strains was higher than that of the other enterococci species, except Enterococcus avium strains. Within lactobacilli strains, the highest mean proteolytic activity was that of Lactobacillus bifermentans, Lactobacillus brevis and Lactobacillus casei strains.

Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California

Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated with AOA group A amoA gene copies (r2=0.90, P<0.001), and with 16S rRNA gene copies from marine Crenarchaeota (r2=0.85, P<0.005). These findings represent compelling evidence for an archaeal role in oceanic nitrification.