Restriction Fragment Length Polymorphism Fingerprinting Research Articles

Molecular identification of Candida species isolated from candiduria and its risk factors in neonates and children.

Background and Purpose: The present study was performed to raise attention on the frequency of Candida spp. and evaluation of risk factors of candiduria in neonates and children.Materials and Methods: In total, 60 urine samples were collected from the suspected neonates and children. Identification of Candida at species level was performed using the polymerase chain reaction-restriction fragment length polymorphism approach. Results: The restriction fragment length polymorphism fingerprint analysis revealed that Candida parapsilosis (n=17; 28.33 %) is the most prevalent isolated species followed by Candida albicans (n=9; 15%), Candida tropicalis (n=4; 9.52%), and C. glabrata (n=2; 4.76%). All of the C. albicans and C. parapsilosis complex strains were identified as C. albicans with HWP1 gene primers and using the NlaIII restriction enzyme activity, respectively. In this study, none of the mentioned factors was the cause of infection, but they could be considered risk factors. The mean hospital stay was 21 days (range: 7-21 days). More than 90% of the patients had a urinary catheter, and about 26% of them received antibiotics. Regarding the risk factors, there was no significant difference between the two groups of candidiasis in terms of C. albicans and non-albicans Candida (P<0.01). Conclusion: Candiduria has always been a challenging issue, especially in children admitted to hospitals. Outcome of candiduria in patients with generally healthy is little.

Herbivory and Soil Water Availability Induce Changes in Arbuscular Mycorrhizal Fungal Abundance and Composition.

We tested the prediction that abundance and composition of arbuscular mycorrhizal fungi (AMF) in Ipomopsis aggregata roots and soils are influenced by ungulate herbivory and drought conditions by examining the effects in a field setting over two years. We used a multi-metric approach to quantify AMF root colonization, AMF reproduction, and AMF community composition in roots and soils. We incorporated complimentary community characterization assays by morphologically identifying spores from trap cultures and the use of terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Herbivory caused a twofold increase in spore production, an increase in AMF taxa diversity in roots, and a shift in AMF species composition in rhizosphere soils. The impact of herbivory was dependent on water availability, which differed in the two contrasting years. This study demonstrates that both soil water availability and herbivory shape arbuscular mycorrhizal fungi communities. The changes to mycorrhizal communities may help in understanding mycorrhizal function in changing climates.

Key drivers of microbial abundance, activity, and diversity in karst spring waters across an altitudinal gradient in Slovenia

In aquatic ecosystems, the biomass, activity and composition of microorganisms are determined to a large extent by local and regional environmental conditions. While karst aquifers are an important source for drinking water, the ecology of microbial communities in karst waters has hardly been studied. This study examined the regional variations and seasonal dynamics of microbial communities in pristine karst spring waters of Slovenia (Central Europe). Fifteen springs distributed across 5 eco-regions exhibiting a strong altitudinal gradient were sampled 4 times a year. Evaluation of the microbial communities included quantification of prokaryotic biomass via total cell counts and microbial activity estimated via measurements of electron transport system activity. The taxonomic structure of the bacterial communities was analysed by terminal restriction fragment length polymorphism fingerprinting. Biological measures were complemented by a set of physico-chemical parameters, including dissolved organic carbon, nutrients, major ions, temperature, electrical conductivity, pH, and dissolved oxygen. Bacterial community structure differed significantly with seasons and eco-regions, with the latter causing greater variation. While the overall power of the environmental variable tested was a moderate factor (15%) in explaining the variability in microbial community structure, catchment altitude was a key determinant. Prokaryotic cell density and microbial activity in spring water decreased with an increase in catchment altitude and were significantly positively correlated. For a better understanding of karst ecosystems and the ecosystem service of water purification, future investigation should address karst microbial communities at a higher phylogenetic and functional resolution.

Planktonic and Benthic Bacterial Communities of the Largest Central European Shallow Lake, Lake Balaton and Its Main Inflow Zala River

Lake Balaton is the largest European shallow lake, which underwent cultural eutrophication in the ‘70–80s. Therefore, strict pollution control measures were introduced and the water quality has become meso-eutrophic since the millennium. Due to the touristic significance and change in trophic levels of the lake, numerous ecological studies were carried out, but none of them was focused on both benthic and planktonic microbial communities at the same time. In our study, an attempt was made to reveal the spatial bacterial heterogeneity of the Lake Balaton and Zala River by 16S rDNA terminal restriction fragment length polymorphism fingerprinting and Illumina amplicon sequencing methods in the summer of 2017. According to the molecular biology results, mostly well-known freshwater microorganisms, adapted to nutrient-poor conditions were found in the pelagic water column. The LD12 subclade member Fonsibacter ubiquis, the cyanobacterial Synechococcus sp. and unknown Verrucomicrobia species were abundant in the less nutrient-dense basins, while the hgcI clade members showed various distribution. In the estuary and in the nutrient-dense western part of the lake, some eutrophic conditions preferring cyanobacteria (filamentous Anabaena and Aphanizomenon species) were also detectable. The benthic microbial community showed higher diversity, according to the observed appearance of microorganisms adapted to the deeper, less aerated layers (e.g. members of Desulfobacteraceae, Nitrosomonadaceae).

Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

Soil microbial communities are involved in the maintenance of productivity and health of agricultural systems; therefore an adequate understanding of soil biodiversity plays a key role in ensuring sustainable use of soil. In the present study, we evaluated the influence of different cropping systems on the biodiversity of the soil bacterial communities, based on a 54-year field experiment established in Martonvásár, Hungary. Terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique was used to assess soil bacterial diversity and community structure in maize monoculture and three different crop rotations (maize–alfalfa, maize–wheat and the maize–barley–peas–wheat Norfolk type). No differences in richness and diversity were detected between maize monoculture and crop rotations except for the most intense rotation system (Norfolk-type). Although the principal component analysis did not reveal a clear separation between maize monoculture and the other rotation systems, the pairwise tests of analysis of similarity (ANOSIM) revealed that there are significant differences in the composition of bacterial communities between the maize monoculture and maize–alfalfa rotation as well as between wheat–maize and Norfolk-type rotation.

A submerged membrane bioreactor under unprecedentedly short hydraulic retention time enabled by non-woven fabric pre-filtration and electrochemical membrane cleaning

This study reports that electrochemical oxidation (EO) coupled with non-woven fabric (NWF) filter synergistically mitigated fouling in a submerged membrane bioreactor (MBR) under hydraulic retention time (HRT) of 1 h. Our NWF-EO-MBR was equipped with NWF prefilter cage surrounding microfiltration (MF) membrane with IrO2 anodes in vicinity. Continuous operation showed a retarded increase of transmembrane pressure at intermittent current density (5 mA cm−2) to prolong operation duration by 40% under constant flux (13.75 L m−2 h−1). Primary separation of bio-flocs by NWF not only reduced physically removable fouling on MF, but also allowed augmented concentration of electrolytic free chlorine (FC) near 4.0 mgCl2 L−1 inside the NWF cage. The FC degraded dissolved foulants to reduce physically irremovable hydraulic resistance of MF. A limited nitrification under the short HRT was assisted by electrochemical breakpoint chlorination, resulting 72% total nitrogen removal efficiency on average. Terminal restriction fragment length polymorphism fingerprinting indicated that the microbial community in mixed liquor was less influenced by FC than that in bio-cake on MF. The energy consumption of EO was approximated to 28 Wh per m3 of permeate.

Genetic diversity and symbiotic efficiency difference of endophytic rhizobia of Medicago sativa.

Research on rhizobium diversity has paved the way for diversification of rhizobial germplasm resources. Seventy-three endophytic bacterial isolates were collected from seven tissues of five alfalfa cultivars in three geographic locations in Gansu, China. Restriction fragment length polymorphism (RFLP) fingerprinting of 16S rRNA and analysis of concatenated sequence of three housekeeping genes (atpD, glnII, and recA) and two symbiotic genes (nodC and nifH) were used for strain identification. Results showed that the endophytic strains were genetically diverse at different taxonomic levels, and Ensifer meliloti (31) and Agrobacterium radiobacter (12) are common Medicago sativa endophytic bacteria in Gansu, China. The nifH genes (97%-98% sequence identity) of E. meliloti strains were more diverse than the nodC genes (99%-100% sequence identity), even though the strains evolved from a common ancestor. The degree of dispersion of symbiotic phenotypes of E. meliloti strains on M. sativa 'Gannong No. 3', 'Gannong No. 9', and 'Qingshui' was much less than that on M. sativa 'Longzhong' and 'WL168HQ'. This suggested that the symbiotic efficiency of E. meliloti strains on the former three alfalfa cultivars was similar but on the latter two was discrepant. Their symbiotic efficiency differed primarily according to alfalfa cultivars and, to a lesser extent, to the tested strains, indicating the difference in the sensitivity of different alfalfa cultivars to rhizobial strains.

Diversity and symbiotic divergence of endophytic and non-endophytic rhizobia of Medicago sativa

Knowledge of rhizobium diversity is helping to enable the utilization of rhizobial resources. To analyze the phenotypic and genetic diversity and the symbiotic divergence of rhizobia of Medicago sativa, 30 endophytic and non-endophytic isolates were collected from different parts of five alfalfa varieties in three geographic locations in Gansu, China. Numerical analyses based on 72 phenotypic properties and restriction fragment length polymorphism (RFLP) fingerprinting indicated the abundant phenotypic and genetic diversity of the tested strains. According to the phylogenetic analysis of 16S RNA, atpD, glnII, and recA gene sequences, Rhizobium and Ensifer were further classified into four different genotypes: Rhizobium radiobacter, Rhizobium sp., Rhizobium rosettiformans, and Ensifer meliloti. The differences in architecture and functioning of the rhizobial genomes and, to a lesser extent, environment diversification helped explain the diversity of tested strains. The tested strains exhibited similar symbiotic feature when inoculated onto M. sativa cvs. Gannong Nos. 3 and 9 and Qingshui plants for the clustering feature of their parameter values. An obvious symbiotic divergence of rhizobial strains was observed in M. sativa cvs. Longzhong and WL168HQ plants because of the scattered parameter values. Their symbiotic divergence differed according to alfalfa varieties, which indicated that the sensitivity of different alfalfa varieties to rhizobial strains may differ. Most of the tested strains exhibited plant growth-promoting traits including phosphate solubilization and production of indole-3-acetic acid (IAA) when colonizing plant tissues and soil.

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments.

The aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.

Methanogenic community composition in an organic waste mixture in an anaerobic bioreactor

AbstractThe aim of the study was to elucidate the substantial relationship between the compositions of methanogen community that assembles in the anaerobic digester mass and link it to methane production activity. The results of the metagenomic studies were used to evaluate how the methanogen structure changes during an anaerobic digestion process under various waste retention times (21, 23, 25, 29, 33, 39, 47 and 61 days). Phylogenetically coherent populations of methanogens were assessed by 16S rRNA gene next-generation sequencing and terminal restriction fragment length polymorphism fingerprinting of a specific molecular marker, themcrAgene. The results indicated multiple phylogenetically diverse methanogen populations associated with the various steps of anaerobic digestion. The stages of the anaerobic digestion process and waste retention times determine the microbial composition. The most dominant and acclimated microbial communities in all samples belonged to the generaMethanosaetaandMethanobacterium.The methane yield was consistent with the results of the microbial community structure, which indicated that acetotrophicMethanosaetawas the most active and most important during the methanogenic stage.

Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient.

The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.

Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw

The aim of this study was to determine the potential of bioaugmentation with cellulolytic rumen microbiota to enhance the anaerobic digestion of lignocellulosic feedstock. An anaerobic cellulolytic culture was enriched from sheep rumen fluid using wheat straw as substrate under mesophilic conditions. To investigate the effects of bioaugmentation on methane production from straw, the enrichment culture was added to batch reactors in proportions of 2% (Set-1) and 4% (Set-2) of the microbial cell number of the standard inoculum slurry. The methane production in the bioaugmented reactors was higher than in the control reactors. After 30 days of batch incubation, the average methane yield was 154 mLN CH4 gVS−1 in the control reactors. Addition of 2% enrichment culture did not enhance methane production, whereas in Set-2 the methane yield was increased by 27%. The bacterial communities were examined by 454 amplicon sequencing of 16S rRNA genes, while terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of mcrA genes was applied to analyze the methanogenic communities. The results highlighted that relative abundances of Ruminococcaceae and Lachnospiraceae increased during the enrichment. However, Cloacamonaceae, which were abundant in the standard inoculum, dominated the bacterial communities of all batch reactors. T-RFLP profiles revealed that Methanobacteriales were predominant in the rumen fluid, whereas the enrichment culture was dominated by Methanosarcinales. In the batch rectors, the most abundant methanogens were affiliated to Methanobacteriales and Methanomicrobiales. Our results suggest that bioaugmentation with sheep rumen enrichment cultures can enhance the performance of digesters treating lignocellulosic feedstock.

Microbial diversity and community structure of denitrifying biological filters operated with different carbon sources

The treatment performance and spatial microbial community structure of three parallel denitrifying biological filters (DNBFs) operated with methanol, ethanol and acetate, respectively, were explored. The acetate-fed DNBF presented the highest denitrification rate and NOx-N (NO2-N and NO3-N) removal efficiency, while the methanol-fed DNBF showed the lowest carbon consumption and NOx-N removal efficiency. Distinct spatial distribution patterns of terminal restriction fragment length polymorphism fingerprints were observed among the DNBFs. The ethanol enhanced captured biofilms throughout the flowpath of DNBF had the highest diversity and evenness. The methanol-enhanced attached biofilm along the flowpath presented the highest evenness, but lowest richness and limited diversity. β-Proteobacteria was dominant in the microbial community in all of methanol, ethanol and acetate enhanced biofilm; however, different external carbon sources resulted in different dominant genera species. Thauera was dominant in the acetate enhanced bacterial community, while both Dechloromonas and Thauera were dominant in that of ethanol fed. However, methylotrophic bacteria (Methyloversatilis and Methylotenera) dominated exclusively in the methanol enhanced bacterial community throughout of the DNBF.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3451-3) contains supplementary material, which is available to authorized users.

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R=0.786, P=0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R=0.194, P=0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment

Membrane bioreactors (MBRs) were operated on-site for 56d with different powdered activated carbon (PAC) dosages of 0, 1.5 and 5.0g/L to pretreat seawater for reverse osmosis desalination. It was hypothesized that PAC would stimulate adsorption and biological degradation of organic compounds. The microbial communities responsible for biofouling on microfiltration (MF) membranes and biological organic removal in MBR were assessed using terminal restriction fragment length polymorphism fingerprinting and 454-pyrosequencing. The PAC addition improved assimilable organic carbon removal (53–59%), and resulted in reduced biofouling development on MF (>50%) with only a marginal development in trans-membrane pressure. Interestingly, the bacterial community composition was significantly differentiated by the PAC addition. Cyanobacterium, Pelagibaca and Maricoccus were dominant in the PAC-free conditions, while Thiothrix and Sphingomonas were presumably responsible for the better reactor performances in PAC-added conditions. In contrast, the archaeal communities were consistent with predominance of Candidatus Nitrosopumilus. These data therefore show that the addition of PAC can improve MBR performance by developing different bacterial species, controlling AOC and associated biofouling on the membranes.

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.

Diversity of Methane-Oxidizing Bacteria in Soils from "Hot Lands of Medolla" (Italy) Featured by Anomalous High-Temperatures and Biogenic CO2 Emission.

“Terre Calde di Medolla” (TCM) (literally, “Hot Lands of Medolla”) refers to a farming area in Italy with anomalously high temperatures and diffuse emissions of biogenic CO2, which has been linked to CH4 oxidation processes from a depth of 0.7 m to the surface. We herein assessed the composition of the total bacterial community and diversity of methane-oxidizing bacteria (MOB) in soil samples collected at a depth at which the peak temperature was detected (0.6 m). Cultivation-independent methods were used, such as: i) a clone library analysis of the 16S rRNA gene and pmoA (coding for the α-subunit of the particulate methane monooxygenase) gene, and ii) Terminal Restriction Fragment Length Polymorphism (T-RFLP) fingerprinting. The 16S rRNA gene analysis assessed the predominance of Actinobacteria, Acidobacteria, Proteobacteria, and Bacillus in TCM samples collected at a depth of 0.6 m along with the presence of methanotrophs (Methylocaldum and Methylobacter) and methylotrophs (Methylobacillus). The phylogenetic analysis of pmoA sequences showed the presence of MOB affiliated with Methylomonas, Methylocystis, Methylococcus, and Methylocaldum in addition to as yet uncultivated and uncharacterized methanotrophs. Jaccard’s analysis of T-RFLP profiles at different ground depths revealed a similar MOB composition in soil samples at depths of 0.6 m and 0.7 m, while this similarity was weaker between these samples and those taken at a depth of 2.5 m, in which the genus Methylocaldum was absent. These results correlate the anomalously high temperatures of the farming area of “Terre Calde di Medolla” with the presence of microbial methane-oxidizing bacteria.

Antibacterial, electrospun nanofibers of novel poly(sulfobetaine) and poly(sulfabetaine)s.

Polymers capable of forming hydration layers have gained increasing attention due to their ability to form environmentally friendly antifouling surfaces. Zwitterionic polymers are an important class of materials under this category. However, the effectiveness of many zwitterionic polymers for long-term applications is compromised because of their solubility in sea water, poor hydrolytic stability and deteriorating mechanical integrity upon wetting. This study reports on the preparation and characterization of electrospun fibers derived from novel polysulfobetaine and polysulfabetaines (PSBs) composed of polyvinylbenzyl backbones. The morphology of the electrospun nanofibers was elucidated with the help of a scanning electron microscope. Hydration studies were conducted in deionized water and artificial sea water. Antifouling performance of the electrospun nanofibers was evaluated by studying the adhesion and growth of bacteria in natural, and filtered sea water. Terminal restriction fragment length polymorphism (TRFLP) fingerprinting was performed to determine the nature of the bacterial community attached to the electrospun fibers. Some of the PSBs prevented bacterial growth without showing any biocidal nature. Thus the findings of this study are potentially relevant for current trends seeking environmentally friendly antifouling solutions.

The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters

Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under diverse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria.

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I (“Slash-and-burn deforestation”) the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II (“Management practices for sugarcane”) disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-015-0530-3) contains supplementary material, which is available to authorized users.