Václav Krištůfek

Microbial diversity determines the invasion of soil by a bacterial pathogen

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity–function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invaders fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

Application of ARDRA and PLFA analysis in characterizing the bacterial communities of the food, gut and excrement of saprophagous larvae ofPenthetria holosericea (Diptera: Bibionidae): a pilot study

Amplified ribosomal DNA restriction analysis (ARDRA) was used to compare the bacterial communities of the food, the gut sections (ceca, anterior and posterior midgut, hindgut) and the excrement of the litter feeding bibionid larvae ofPenthetria holosericea. For universal eubacterial primers ARDRA patterns were complex with only minor differences among samples. Taxon specific primers were also applied to characterize the samples. Fragment composition was transformed to presence/absence binary data and further analyzed. Cluster analysis revealed that bacterial communities of gut highly resembled each other with the exception of the ceca. ARDRA patterns of consumed leaves clustered together with the intact leaves but differed from those of the excrement. ARDRA results were compared with microbial community structure based on phospholipid fatty acid (PLFA) fingerprints. The cluster analysis of PLFA (presence/absence binary) data resulted in a pattern similar to the ARDRA data. The PCA analysis of PLFA relative content separated microbial communities into five groups: (1) anterior and posterior midgut, (2) hindgut, (3) ceca, (4) consumed and intact litter, (5) excrement. Both methods indicated that conditions in the larval gut result in formation of a specific microbial community which differs from both the food and excrement ones. Particularly ceca — (blind appendages, harbor very specific microbial community) are divided from the rest of the gut by perithropic membrane.

Growth strategy of heterotrophic bacterial population along successional sequence on spoil of brown coal colliery substrate

The bacterial population of brown coal colliery spoil (Sokolov coal mining district, Czechia) was characterized by measuring viable bacterial biomass, the culturable to total cell ratio (C:T), colony-forming curve (CFC) analysis and species and/or biotype diversity. Bacterial representatives that differed in colony-forming growth (fast and/or slow growers) were used for growth-strategy investigation of heterotrophic bacteria. Spoil substrates from the surface (0–50 mm) and the mineral (100–150 mm) layers were sampled on 4 sites undergoing spontaneous succession corresponding to 1, 11, 21 and 43 years after deposition (initial, early, mid and late stages). The bacterial biomass of the surface layer increased during the initial and early stages with a maximum at mid stage and stabilized in the late stage while mineral layer biomass increased throughout the succession. The maxima of C:T ratios were at the early stage, minima at the late stage. Depending on the succession stage the C:T ratio was 1.5–2 times higher in the mineral than the surface layer of soil. An increase in the fraction of nonculturable bacteria was associated with the late succession stage. CFC analysis of the surface layer during a 3-d incubation revealed that the early-succession substrate contained more (75 %) rapidly colonizing bacteria (opportunists, r-strategists) than successively older substrates. The culturable bacterial community of the mineral layer maintained a high genera and species richness of fast growers along the succession line in contrast to the surface layer community, where there was a maximum in the abundance of fast growers in the early stage. There was a balanced distribution of Grampositive and Gram-negative representatives of fast growers in both layers. A markedly lower abundance of slow growers was observed in the mineral in contrast to the surface layer. Gram-positive species dominated the slow growers at the surface as well as in the mineral layers. The growth strategy of the heterotrophic bacterial population along four successional stages on spoil of brown coal colliery substrate in the surface layer displayed a trend indicative of a r-K continuum in contrast to the mineral layer, where an r-strategy persisted.

Land use intensity controls actinobacterial community structure

Actinobacteria are major producers of secondary metabolites; however, it is unclear how they are distributed in the environment. DNA was extracted from forest, pasture and cultivated soils, street sediments (dust and material in place), and sediments affected by animal activity (e.g. guano, vermicompost) and characterised with two actinobacterial and a bacterial-specific 16S rDNA primer set. Amplicons (140/156) generated with the two actinobacterial-specific and amplicons (471) generated with bacterial-specific primers were analysed. Amplicons from actinobacterial-specific primer were disproportionately actinomycetal from animal-affected (soil) samples and street sediments and either verrucomicrobial (i.e. non-actinobacterial) and from a novel non-actinomycetal actinobacterial group for soils. Actinobacterial amplified ribosomal DNA restriction analysis and terminal restriction fragment length polymorphism fingerprints clustered by land use, with cultivated soils clustering apart from uncultivated soils. Actinobacterial amplicons generated with eubacterial primers were overwhelmingly from (116/126) street sediments; acidobacterial amplicons from soils (74/75). In two street samples, >90% of clones were actinomycetal. Actinomycetes are selected in terrestrial soils and sediments by cultivation, urbanisation and animal activity.

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

BackgroundHost plant roots, mycorrhizal mycelium and microbes are important and potentially interacting factors shaping the performance of mycorrhization helper bacteria (MHB). We investigated the impact of a soil microbial community on the interaction between the extraradical mycelium of the ectomycorrhizal fungus Piloderma croceum and the MHB Streptomyces sp. AcH 505 in both the presence and the absence of pedunculate oak microcuttings.ResultsSpecific primers were designed to target the internal transcribed spacer of the rDNA and an intergenic region between two protein encoding genes of P. croceum and the intergenic region between the gyrA and gyrB genes of AcH 505. These primers were used to perform real-time PCR with DNA extracted from soil samples. With a sensitivity of 10 genome copies and a linear range of 6 orders of magnitude, these real-time PCR assays enabled the quantification of purified DNA from P. croceum and AcH 505, respectively. In soil microcosms, the fungal PCR signal was not affected by AcH 505 in the absence of the host plant. However, the fungal signal became weaker in the presence of the plant. This decrease was only observed in microbial filtrate amended microcosms. In contrast, the PCR signal of AcH 505 increased in the presence of P. croceum. The increase was not significant in sterile microcosms that contained plant roots.ConclusionsReal-time quantitative PCR assays provide a method for directly detecting and quantifying MHB and mycorrhizal fungi in plant microcosms. Our study indicates that the presence of microorganisms and plant roots can both affect the nature of MHB-fungus interactions, and that mycorrhizal fungi may enhance MHB growth.

Changes in amount of bacteria during gut passage of leaf litter and during coprophagy in three species of Bibionidae (Diptera) larvae

To elucidate the interaction between bacteria and saprophagousDiptera larvae, the amounts of bacteria in leaf litter, individual gut compartments, and feces of three species ofBibionidae (Bibio pomonae, Bibio marci, andPenthetria holosericea), feeding either directly on leaf litter or on fecal pellets produced from leaf litter by larvae of the same species, were assessed by determining total direct counts and viable counts on solid media at different pH. InP. holosericea, the effect of various cultivation temperatures on direct counts of bacteria in individual compartments was also demonstrated. In all species, the amount of bacteria in the anterior mesenteron was lower than in the consumed food, regardless of whether the larvae were feeding on leaf litter or feces, and increased again in the posterior part of the gut. The amount of bacteria in these compartments was generally higher in larvae feeding on feces than in those feeding on leaf litter, whereas the amount of bacteria found in the ceca varied. InB. marci, the amount of bacteria in the mesenteron sections able to grow on alkaline medium (pH 9) was higher than that of bacteria able to grow on slightly acidic medium (pH 5.5) during both the first and the second gut passage. InB. pomonae andP. holosericea, this increase was observed only during the second gut passage. The effect of gut passage inP. holosericea on changes in direct counts of bacteria was more pronounced when the larvae were fed at 5 °C as compared to 20 °C. Radiolabeled bacteria were digested in the gut and utilized as a source of energy and nutrients by the larvae; digested bacteria represented up to 10 % of the material assimilated by the larvae. Lysozyme activity in whole-gut extracts ofP. holosericea had a pH optimum of at pH 7, indicating a lowin situ activity in the alkaline mesenteron. Proteinase activity, however, had an optimum at pH >12, suggesting that the digestion of bacteria in the bibionid gut is caused by a combination of digestive proteinases and alkaline pH in the anterior mesenteron.

Diverse Archaeal Community of a Bat Guano Pile in Domica Cave (Slovak Karst, Slovakia)

The molecular diversity of Archaea in a bat guano pile in Cave Domica (Slovakia), temperate cave ecosystem with significant bat colony (about 1600 individuals), was examined. The guano pile was created mainly by an activity of the Mediterranean horseshoe bat (Rhinolophus euryale) and provides a source of organic carbon and other nutrients in the oligotrophic subsurface ecosystem. The upper and the basal parts of guano surface were sampled where the latter one had higher pH and higher admixture of limestone bedrock and increased colonization of invertebrates. The relative proportion of Archaea determined using CARD-FISH in both parts was 3.5–3.9 % (the basal and upper part, respectively). The archaeal community was dominated by non-thermophilic Crenarchaeota (99 % of clones). Phylogenetic analysis of 115 16S rDNA sequences revealed the presence of Crenarchaeota previously isolated from temperate surface soils (group 1.1b, 62 clones), deep subsurface acid waters (group 1.1a, 52 clones) and Euryarchaeota (1 clone). Four of the analyzed sequences were found to have little similarity to those in public databases. The composition of both archaeal communities differed, with respect to higher diversity of Archaea in the upper part of the bat guano pile. High diversity archaeal population is present in the bat guano deposit and consists of both soil- and subsurface-born Crenarchaeota.

Preliminary data about compartmentalization of the gut of the saprophagous dipteran larvae Penthetria holosericea (Bibionidae)

Abstract To describe the compartmentalization of the gut and the microbial activity in the digestive tract, the histology of the gut wall, enzymatic activity, pH of the gut content, abundance and composition of the microbial community (direct counts, plate counts on various media, and phospholipid fatty acid analyses—PLFA) were studied in the Penthetria holosericea larvae. The highest secretion activity was observed in the caeca and in the part of the anterior midgut before caeca openings. A strong increase in pH (10.5) was observed in the anterior part of the midgut. Some enzymes produced in the caeca might have their maximum activity in a different part of the gut as a result of their pH optimum; e.g. amylase was most active in the strongly alkaline anterior part of the mesenteron. Maltase, hydrolyzing products of starch degradation, was most active in the posterior part of the gut and in the ectoperithrophic space. The microbial community was reduced in the anterior part of the midgut. In the posterior part of the gut, bacterial numbers increased and peaked in excrements. Caeca had an abundant microbial community.

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites.

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm3 of tertiary alkaline clay sediment from Sokolov brown‐coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential in comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N)2 fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara.

The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils.

Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.