A microtiter plate procedure for evaluating fungal functional diversity

Can soil health in degraded woodlands of a semi-arid environment improve after thirty years?

In natural habitats, especially in arid and semi-arid areas that are fragile ecosystems, vegetation degradation is one of the most important factors affecting the variability of soil health. Studying physicochemical and biological parameters that serve as indicators of soil health offers important information on the potential risk of land degradation and the progression of changes in soil performance and health during recovery periods. This study specifically examines the impact of vegetation degradation on soil health indicators and the duration needed to improve the physical, chemical, and biological parameters in a semi-arid mountainous area site types with the dominance of Quercus macranthera Fisch & C.A. Mey and Carpinus orientalis Miller in northern Iran. In different years (2003, 2013, and 2023), litter and soil samples (at depths of 0-10, 10-20, and 20-30 cm) were collected in different types of degraded sites. Additionally, in 2023, a non-degraded site was chosen as a control and similar samples were collected. A total of 48 litter (12 samples for each of the study site types) and 144 soil (4 study site types × 3 depths × 12 samples) samples were collected. In order to investigate the spatial changes of soil basal respiration (or CO2 emission), which is involved in global warming, from each site type, 50 soil samples were taken along two 250-meter transects. The findings showed that litter P and Mg contents in the non-degraded site were 1.6 times higher than in degraded site types (2003). Following vegetation degradation, soil fertility indicators decreased by 2-4 times. The biota population was lower by about 80 % under the degraded site types (2003) than in the non-degraded site, and the density of fungi and bacteria in the degraded site types was almost half that of the non-degraded site types. Geostatistics showed the high variance (linear model) of CO2 emissions in areas without degradation. In addition, vegetation degradation significantly reduced soil carbon and nitrogen mineralization. Although soil health indicators under the degraded vegetation have improved over time (30 years), results showed that even thirty years is not enough for the full recovery of a degraded ecosystem, and more time is needed for the degraded area to reach the same conditions as the non-degraded site. Considering the time required for natural restoration in degraded site types, it is necessary to prioritize the conservation of vegetation and improve the ecosystem restoration process with adequate interventions.

Comprehensive antifungal investigation of natural plant extracts against Neosartorya spp. (Aspergillus spp.) of agriculturally significant microbiological contaminants and shaping their metabolic profile

Fungi belonging to the genus Neosartorya (teleomorph of Aspergillus spp.) are of great concern in the production and storage of berries and fruit-based products, mainly due to the production of thermoresistant ascospores that cause food spoilage and possible secretion of mycotoxins. We initially tested the antifungal effect of six natural extracts against 20 isolates of Neosartorya spp. using a traditional inhibition test on Petri dishes. Tested isolates did not respond uniformly, creating 5 groups of descending sensitivity. Ten isolates best representing of the established sensitivity clusters were chosen for further investigation using a Biolog™ MT2 microplate assay with the same 6 natural extracts. Additionally, to test for metabolic profile changes, we used a Biolog™ FF microplate assay after pre-incubation with marigold extract. All natural extracts had an inhibitory effect on Neosartorya spp. growth and impacted its metabolism. Lavender and tea tree oil extracts at a concentration of 1000 µg mL-1 presented the strongest antifungal effect during the inhibition test, however all extracts exhibited inhibitory properties at even the lowest dose (5 µg mL-1). The fungal stress response in the presence of marigold extract was characterized by a decrease of amino acids and carbohydrates consumption and an uptake of carboxylic acids on the FF microplates, where the 10 studied isolates also presented differences in their innate resilience, creating 3 distinctive sensitivity groups of high, average and low sensitivity. The results confirm that natural plant extracts and essential oils inhibit and alter the growth and metabolism of Neosartorya spp. suggesting a possible future use in sustainable agriculture as an alternative to chemical fungicides used in traditional crop protection.

Ant nests as a microbial hot spots in a long-term heavy metal-contaminated soils

Interactions between soil fauna and soil microorganisms are not fully recognized, especially in extreme environments, such as long-term metal-polluted soils. The purpose of the study was to assess how the presence of Lasius niger ants affected soil microbial characteristics in a long-term metal-polluted area (Upper Silesia in Poland). Paired soil samples were taken from bulk soil and from ant nests and analysed for a range of soil physicochemical properties, including metal content (zinc, cadmium, and lead). Microbial analysis included soil microbial activity (soil respiration rate), microbial biomass (substrate-induced respiration rate), and bacteria catabolic properties (Biolog^® ECO plates). Soil collected from ant nests was drier and was characterized by a lower content of organic matter, carbon and nitrogen contents, and also lower metal content than bulk soil. Soil microbial respiration rate was positively related to soil pH (p = 0.01) and negatively to water-soluble metal content, integrated into TI_ws index (p = 0.01). Soil microbial biomass was negatively related to TI_ws index (p = 0.04). Neither soil microbial activity and biomass nor bacteria catabolic activity and diversity indices differed between bulk soil and ant nests. Taken together, ant activity reduced soil contamination by metals in a microscale which support microbial community activity and biomass but did not affect Biolog® culturable bacteria.

Elevated temperature may reduce functional but not taxonomic diversity of fungal assemblages on decomposing leaf litter in streams

Mounting evidence points to a linkage between biodiversity and ecosystem functioning (B-EF). Global drivers, such as warming and nutrient enrichment, can alter species richness and composition of aquatic fungal assemblages associated with leaf-litter decomposition, a key ecosystem process in headwater streams. However, effects of biodiversity changes on ecosystem functions might be countered by the presumed high functional redundancy of fungal species. Here, we examined how environmental variables and leaf-litter traits (based on leaf chemistry) affect taxonomic and functional α- and β-diversity of fungal decomposers. We analysed taxonomic diversity (DNA-fingerprinting profiles) and functional diversity (community-level physiological profiles) of fungal communities in four leaf-litter species from four subregions differing in stream-water characteristics and riparian vegetation. We hypothesized that increasing stream-water temperature and nutrients would alter taxonomic diversity more than functional diversity due to the functional redundancy among aquatic fungi. Contrary to our expectations, fungal taxonomic diversity varied little with stream-water characteristics across subregions, and instead taxon replacement occurred. Overall taxonomic β-diversity was fourfold higher than functional diversity, suggesting a high degree of functional redundancy among aquatic fungi. Elevated temperature appeared to boost assemblage uniqueness by increasing β-diversity while the increase in nutrient concentrations appeared to homogenize fungal assemblages. Functional richness showed a negative relationship with temperature. Nonetheless, a positive relationship between leaf-litter decomposition and functional richness suggests higher carbon use efficiency of fungal communities in cold waters.

Soil Enzyme Activity and Microbial Metabolic Function Diversity in Soda Saline–Alkali Rice Paddy Fields of Northeast China

Western Jilin province has the most serious area of soda salinization in Northeast China, which affects and restricts the sustainable development of agriculture. The effects of physico-chemical properties of rhizosphere and non-rhizosphere soil on soil microbial diversity and enzyme activities (polyphenol oxidase, catalase, invertase, amylase) were evaluated in typical soda saline-alkali paddy field. Community-level physiological profile (CLPP) based on Biolog-ECO plates was used to assess the functional diversity of soil microorganisms. Exchangeable sodium percentage (ESP) and pH were negative correlated with the microbial activity (AWCD), soil enzyme activities (amylase, sucrose, and catalase, except for polyphenol oxidase) in rice rhizosphere and non-rhizosphere soil (P < 0.05). The indexes of microbial diversity in rice rhizosphere soil were significantly higher than that of non-rhizosphere soil. The utilization of amino acids by rice rhizosphere microorganisms was relatively high, while non-rhizosphere soil had relatively high utilization of carboxylic acid, phenolic acid, and amine. Among the selected physico-chemical properties, soil organic carbon (SOC) and soil water content (SWC) had the greatest influence on the variation of microbial diversity indexes and enzyme activities in rhizosphere soil. ESP and pH showed a significant positive correlation with carbon source utilization, especially for amine (AM) and phenolic acid (PA) carbon source utilization (P < 0.05) by means of RDA, and the utilization rate of AM and PA carbon sources by rice rhizosphere and non-root soil microorganisms was P1 < P2 < P3.

Comparative eco-physiology revealed extensive enzymatic curtailment, lipases production and strong conidial resilience of the bat pathogenic fungus Pseudogymnoascus destructans

The genus Pseudogymnoascus encompasses soil psychrophilic fungi living also in caves. Some are opportunistic pathogens; nevertheless, they do not cause outbreaks. Pseudogymnoascus destructans is the causative agent of the white-nose syndrome, which is decimating cave-hibernating bats. We used comparative eco-physiology to contrast the enzymatic potential and conidial resilience of P. destructans with that of phylogenetically diverse cave fungi, including Pseudogymnoascus spp., dermatophytes and outdoor saprotrophs. Enzymatic potential was assessed by Biolog MicroArray and by growth on labelled substrates and conidial viability was detected by flow cytometry. Pseudogymnoascus destructans was specific by extensive losses of metabolic variability and by ability of lipid degradation. We suppose that lipases are important enzymes allowing fungal hyphae to digest and invade the skin. Pseudogymnoascus destructans prefers nitrogenous substrates occurring in bat skin and lipids. Additionally, P. destructans alkalizes growth medium, which points to another possible virulence mechanism. Temperature above 30 °C substantially decreases conidial viability of cave fungi including P. destructans. Nevertheless, survival of P. destructans conidia prolongs by the temperature regime simulating beginning of the flight season, what suggests that conidia could persist on the body surface of bats and contribute to disease spreading during bats active season.

Diversity and function of the microbial community under strong selective pressure of rotifers

We unearthed some interesting microecological discoveries while selecting for the most beneficial bacterial strains to be used as probiotics in Lecane inermis rotifer mass culture. For 3 years, we maintained the cultures of L. inermis, with selection for the highest growth rate and resistance to potential contamination. Then, we conducted further selection and isolation in two groups: rotifers inoculated with the bacterial consortium isolated from the rotifer cultures, and rotifers fed with a commercial bioproduct. Selection was conducted in demanding conditions, with particulate matter suspended in spring water as a substrate, without aeration and under strong consumer pressure, and led to selection of two cultivable strains isolated from the optimal rotifers culture. According to molecular analysis, these strains were Aeromonas veronii and Pseudomonas mosselii. Biolog® ECO plate tests showed that both investigated bacterial communities metabolized wide but similar range of substrates. Therefore, intensely selective conditions led to considerable reduction in bacterial community regarding taxonomy, but not in metabolic activity, showing a functional composition decoupling. Aside from this result, our novel selection method dedicated to the sustainable culture of two trophic levels, a directed selection procedure (DSC), could potentially lead to the development of biotechnologically valuable strains with high metabolic activity and the ability to metabolize different sorts of substrate without harmful impact on higher trophic levels.

Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.

Assessment of water samples with complex compositions using microalgal bioassay based on the community level physiological profiling (CLPP)

The ability to effectively characterize the response of microalgal communities to changes in water quality is limited. Earlier, a microalgal bioassay was developed based on community level physiological profiling (CLPP). The efficacy of this assay was evaluated using three wetland water samples, a surface water sample, and two wastewater samples (i.e. primary and secondary), all collected from southwestern Ontario, Canada. In addition, the assay was applied to untreated and activated carbon treated oil sand process water (OSPW). YT (Yeast Identification Test Panel) and Biolog plates were successfully utilized for defined microalgal community under both heterotrophic and mixotrophic growth conditions to characterize the changes in the defined microalgal community due to the changes in water type. It was found that, although the degrees of changes in the algal community varied, all tested water samples were distinguished under both growth regimes using principal component analysis (PCA). The variations in the algal community were caused by the differences of the water samples. The response of the assay due to changes in the algal community caused by different waters was found to be very sensitive and could be used to differentiate different water bodies. It further can be used to monitor temporal changes of water quality of the same water body.

Structural and metabolic responses of microbial community to sewage-borne chlorpyrifos in constructed wetlands

Long-term use of chlorpyrifos poses a potential threat to the environment that cannot be ignored, yet little is known about the succession of substrate microbial communities in constructed wetlands (CWs) under chlorpyrifos stress. Six pilot-scale CW systems receiving artificial wastewater containing 1mg/L chlorpyrifos were established to investigate the effects of chlorpyrifos and wetland vegetation on the microbial metabolism pattern of carbon sources and community structure, using BIOLOG and denaturing gradient gel electrophoresis (DGGE) approaches. Based on our samples, BIOLOG showed that Shannon diversity (H') and richness (S) values distinctly increased after 30days when chlorpyrifos was added. At the same time, differences between the vegetated and the non-vegetated systems disappeared. DGGE profiles indicated that H' and S had no significant differences among four different treatments. The effect of chlorpyrifos on the microbial community was mainly reflected at the physiological level. Principal component analysis (PCA) of both BIOLOG and DGGE showed that added chlorpyrifos made a difference on test results. Meanwhile, there was no difference between the vegetation and no-vegetation treatments after addition of chlorpyrifos at the physiological level. Moreover, the vegetation had no significant effect on the microbial community at the genetic level. Comparisons were made between bacteria in this experiment and other known chlorpyrifos-degrading bacteria. The potential chlorpyrifos-degrading ability of bacteria in situ may be considerable.

A survey of the methods for the characterization of microbial consortia and communities

A survey of the available literature on methods most frequently used for the identification and characterization of microbial strains, communities, or consortia is presented. The advantages and disadvantages of the various methodologies were examined from several perspectives including technical, economic (time and cost), and regulatory. The methods fall into 3 broad categories: molecular biological, biochemical, and microbiological. Molecular biological methods comprise a broad range of techniques that are based on the analysis and differentiation of microbial DNA. This class of methods possesses several distinct advantages. Unlike most other commonly used methods, which require the production of secondary materials via the manipulation of microbial growth, molecular biological methods recover and test their source materials (DNA) directly from the microbial cells themselves, without the requirement for culturing. This eliminates both the time required for growth and the biases associated with cultured growth, which is unavoidably and artificially selective. The recovered nucleic acid can be cloned and sequenced directly or subpopulations can be specifically amplified using polymerase chain reaction (PCR), and subsequently cloned and sequenced. PCR technology, used extensively in forensic science, provides researchers with the unique ability to detect nucleic acids (DNA and RNA) in minute amounts, by amplifying a single target molecule by more than a million-fold. Molecular methods are highly sensitive and allow for a high degree of specificity, which, coupled with the ability to separate similar but distinct DNA molecules, means that a great deal of information can be gleaned from even very complex microbial communities. Biochemical methods are composed of a more varied set of methodologies. These techniques share a reliance on gas chromatography and mass spectrometry to separate and precisely identify a range of biomolecules, or else investigate biochemical properties of key cellular biomolecules. Like the molecular biological methods, some biochemical methods such as lipid analyses are also independent of cultured growth. However, many of these techniques are only capable of producing a profile that is characteristic of the microbial community as a whole, providing no information about individual members of the community. A subset of these methodologies are used to derive taxonomic information from a community sample; these rely on the identification of key subspecies of biomolecules that differ slightly but characteristically between species, genera, and higher biological groupings. However, when the consortium is already growing in chemically defined media (as is often the case with commercial products), the rapidity and relatively low costs of these procedures can mitigate concerns related to culturing biases. Microbiological methods are the most varied and the least useful for characterizing microbial consortia. These methods rely on traditional tools (cell counting, selective growth, and microscopic examination) to provide more general characteristics of the community as a whole, or else to narrow down and identify only a small subset of the members of that community. As with many of the biochemical methods, some of the microbiological methods can fairly rapidly and inexpensively create a community profile, which can be used to compare 2 or more entire consortia. However, for taxonomic identification of individual members, microbiological methods are useful only to screen for the presence of a few key predetermined species, whose preferred growth conditions and morphological characteristics are well defined and reproducible.Key words: microbial communities, microbial consortia, characterization methods, taxonomic identification.