Community-level Physiological Profiles Research Articles

Soil Quality Indices Based on Biological Properties to Assess Chemical Soil Degradation by Metal(loid)s

ABSTRACT Soil quality assessments, rarely applied to contaminated soils with metal(loid)s, consider ecological topics such as multifunctionality, resistance and resilience of microbial communities to perturbations, in addition to ecosystem services. In this study, the effect of metal(loid) contamination was evaluated in soils based on physicochemical and biological properties at different distances from an industrial complex and a Cu smelter. From these properties, soil quality indices (SQIs) were tested to compare their sensitivity and relationship with metal(loid) contamination. Enzyme activities and the average well color development, obtained from the community-level physiological profile, were the most suitable soil quality indicators. These variables along with some physicochemical properties [e.g. total organic carbon, pH, and available metal(loid) contents] were selected to develop SQIs. Five SQIs were calculated, from which the Multifunctionality assessment and the AreaSQI were found to be suitable methods to develop SQIs due to their higher discriminant power and relationship with metal(loid) contamination compared to other SQIs. They were validated using data from the literature, and both showed decreasing values at higher levels of metal(loid) contamination. Although the AreaSQI represents an attractive approach due to its visualization and easy interpretation, the multifunctionality approach showed a stronger sensitivity to chemical degradation by metal(loid)s in soil and offered an easier and faster calculation alternative.

Sensitivity of microbial bioindicators in assessing metal immobilization success in smelter-impacted soils

While plant toxicity reduction remains the primary metric for judging the success of metal immobilization in soil, the suitability of microorganisms as universal indicators of its effectiveness in various contaminated soils remains a point of contention. This study assessed the sensitivity of microbial bioindicators in monitoring metal immobilization success in smelter-impacted soils. It compared plants and microorganisms as indicators of the efficiency of natural Fe-Mn nodules from the Gulf of Finland in immobilizing metals in soils contaminated by a Ni/Cu smelter, on the Kola Peninsula, Murmansk region, Russia. Perennial ryegrass (Lolium perenne) was grown on nodule-amended and control soils. Plant responses in the smelter-impacted soils proved to be sensitive and robust indicators of successful metal immobilization. However, microbial responses exhibited a more complex story. Despite the observed reductions in soluble metal concentrations, shoot metal contents in ryegrass, and significant improvements in plant growth, certain microbial bioindicators were unresponsive to metal immobilization success brought about by the addition of Fe-Mn nodules. Among microbial bioindicators studied, community-level physiological profiling, microbial biomass carbon, and basal respiration were sensitive indicators of metal immobilization success, whereas the number of saprotrophic, oligotrophic, and Fe-oxidizing bacteria and fungi, the biomass of bacteria and fungi, and enzymatic activity were less robust indicators. Interestingly, the correlations between different microbial responses measured were weak or even negative. Some microbial responses also exhibited negative correlations with plant biomass. These findings underscore the need for further research on comparative evaluations of plants and microorganisms as reliable indicators of metal immobilization efficacy in polluted environments.

Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation

Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used chemical fungicide for the control of oomycetes. However, its impact on fungal communities remains unexplored. Therefore, the goal of this study was to examine the effects of mefenoxam on the temporal dynamics of fungal taxonomic and functional diversities during carrot cultivation under four treatment groups: mefenoxam application with and without Pythium inoculation, and untreated control groups with and without Pythium inoculation. Our in vitro sensitivity assay showed that the maximum recommended concentration of mefenoxam, 0.24 ppm, did not suppress the mycelial growth of P. irregulare. At 100 ppm, mycelial growth was only reduced by 11.4%, indicating that the isolate was resistant to mefenoxam. MiSeq sequencing data revealed transient taxonomic variations among treatments 2 weeks post-treatment. Mortierella dominated the fungal community in the mefenoxam-Pythium combination treatment, as confirmed through PCR using our newly designed Mortierella-specific primers. Conversely, mefenoxam-Pythium combination had adverse effects on Penicillium, Trichoderma, and Fusarium, and decrease the overall alpha diversity. However, these compositional changes gradually reverted to those observed in the control by the 12th week. The predicted ecological functions of fungal communities in all Pythium and mefenoxam treatments shifted, leading to a decrease in symbiotrophs and plant pathogen functional groups. Moreover, the community-level physiological profiling approach, utilizing 96-well Biolog FF microplates, showed discernible variations in the utilization of 95 diverse carbon sources among the treatments. Notably, arbutin, l-arabinose, Tween 80, and succinamic acid demonstrated a strong positive association with Mortierella. Our findings demonstrate that a single application of mefenoxam at its recommended rate triggers substantial taxonomic and functional shifts in the soil fungal community. Considering this impact, the conventional agricultural practice of repeated mefenoxam application is likely to exert considerable shifts on the soil ecosystem that may affect agricultural sustainability.

Wine Barrel Biofilm as a Source of Yeasts with Non-Conventional Properties.

This study investigated the main microbial groups characterizing the interior surface of oak barrels from different years (1890, 1895, 1920, 1975, 2008) used in the production of vino cotto. The yeasts were characterized for the following properties: γ-aminobutyric acid (GABA) production, antioxidant activity, air-liquid interfacial biofilm formation, and anthocyanin adsorption capacity. Community-level physiological profile analysis revealed that the microbial communities inside the barrels used the tested carbon sources in different manners. The following yeast species were identified: Millerozyma farinosa, Zygosaccharomyces bisporus, Wickerhamiella versatilis, Zygosaccharomyces bailii, Starmerella lactis-condensi, and Zygosaccharomyces rouxii. All the strains were able to produce GABA, and S. lactis-condensi, Z. bisporus and Z. rouxii were the highest producers (more than 600 mg/L). The Z. rouxii and Z. bailii strains showed the highest antioxidant activity. Only seven strains out of ten M. farinosa formed air-liquid interfacial biofilm. None of the M. farinosa strains adsorbed anthocyanins on their cell wall. The other strains adsorbed anthocyanins in a strain-dependent way, and the highest adsorption was observed for the W. versatilis strains. The yeasts isolated in this study could be used to increase the functional properties and the quality of fermented foods and beverages.

The impact of reclamation and vegetation removal on compositional and functional attributes of soil microbial communities in the Athabasca Oil Sands Region

Large-scale mining for oil extraction in the boreal forests of Northern Alberta has led to a disturbance footprint of ~900 km2 of land; which must be reclaimed to equivalent land capabilities. Microorganisms are sensitive to anthropogenic disturbances and play an essential role in the cycling of soil nutrients and plant growth, making them potential indicators of ecosystem function. Thus, the objective of this work was to determine the impact of land reclamation on the composition and function of soil microbial communities in the Athabasca Oil Sands Region (AOSR). We evaluated bacterial community composition via high throughput sequencing of 16S rRNA genes and soil functional diversity by community-level physiological profiling (CLPP). The ranges of variability for these factors observed in soils reclaimed with either peat-mineral mix (PMM), forest floor-mineral mix (FFM), or FFM diluted with sand (Sand-FFM), were compared to that of undisturbed reference soils (NS) and a vegetation removed soil (VR). Differences between reclamation soils and natural soils were clearly discernible, with reclamation imposing a more drastic disturbance to the boreal forest than that of removal of vegetation alone. VR changed the structure of the soil microbial community and increased the overall diversity, within-community interactions, and heterogeneity; while reclamation shifted the microbial community structure to an even greater extent, placing it outside the range of natural variability. Among reclamation substrates, FFM showed the highest level of similarity to the range of natural variability and PMM showed the least. Altogether, our findings underscore the profound impact of anthropogenic activities associated with large-scale mining on soil biological activity, microbial communities, and edaphic profiles. These alterations are of such magnitude that they render the affected soils significant divergent from the reference undisturbed boreal forest soil.

Bacterial diversity and community level physiological profiling of terasi (Indonesian shrimp paste) to ensure its food safety

Fermentation is a technology to increase the economic value and preserve of seasonal products such as tiny shrimps. This study aimed to ensure the safety and the length of production time of shrimp paste by determining the bacteria involved, during the shrimp paste fermentation process with 10% and 15% salt content. Identification of halophilic bacteria by 16S rRNA used primers 27F and 1492R. Identification of unculturable bacteria used bacterial amplification in the V3-V4 rRNA region. Bacterial activity was observed using the Community Level Physiology Profiling technique. The results showed that the dominant bacteria in shrimp paste with 10% and 15% salt were culturable, i.e., Staphylococcus nepalensis, Salinicoccus qingdaoensis, and Staphylococcus cochnii. In the unculturable identification, the dominant bacteria in shrimp paste with 10% salt were Alkalibacillus, Alkalibacterium, Tetragenococcus, whereas the shrimp paste with 15% salt was dominated by genus of Salimicrobium, Staphylococcus, Corticicoccus, Alkalibacterium and Lentibacillus. The shrimp paste with 10% salt used a high amount of carbohydrate and carboxylic acid substrate. Both 10% and 15% salt of terasi were safe to consume due to no pathogenic bacteria contained. The production of shrimp paste with 10% salt is more profitable due to the low production cost and faster production time.

Assessment of functional diversity of heterotrophic microbial communities in polluted environments through community level physiological profiles

The community level physiological profiles (CLPP) of bacterial communities inhabiting polluted environments (acid mine drainage water and sediments, soils contaminated with tannery waste and oil refinery effluents) were assessed using the Biolog Ecoplates™ in comparison to non-contaminated sites (water and sediments from a recreational lake and soil from anopen space). Although the polluted sites were characterized by typically high metal concentrations, CLPP fingerprints of the different bacterial communities from these sites were indicative of versatile metabolic potentials. These microbial communities could differentially utilize all the different groups of carbon substrates. However, the rates of utilization were significantly lower, and the number of utilized substrates were fewer than those of microbial communities from non-contaminated sites. This was confirmed by cluster analysis in which the dendrogram showed two clusters of microbial communities from contaminated environments and another for those from non-contaminated sites. Nonetheless, the indices of diversity calculated did not show a reduction of diversity or evenness in the microbial communities from contaminated sites. This study confirms the usefulness of the CCLP method in untangling the functional diversity of microbial diversity in contaminated environments.

Exploring the hidden treasures: Deep-sea bacterial community structure in the Bay of Bengal and their metabolic profile

Deep sea bacterial communities demonstrate remarkable adaptability to high-pressure environments coupled with low temperatures which has sparked curiosity about their diversity and exceptional metabolic pathways. Additionally, bacteria in the deep sea exert a substantial influence over various biogeochemical processes. To date, we have relatively very little information about the deep-sea bacterial communities and, they remain largely unexplored. We investigated the variability in the physicochemical conditions, heavy metals and their influence on deep-sea bacterial community structure across three different depths in the Bay of Bengal. The structural and metabolic diversity of deep-sea sediment microbial communities were examined through culture-based sequencing of 16S rRNA genes, ecto-enzymatic studies, and community-level physiological profiling. Bacillota was the most dominant phylum representing 61% of the cultured bacterial isolates, while the remaining belonged to Actinomycetota and Pseudomonodata. Five potential novel species belonging to the genera Fictibacillus, Lysinibacillus, Salinicola, Robertmurraya and Blastococcus were identified. The extracellular enzymatic activity was positive for >50% of the bacterial isolates, wherein the genera Bacillus and Micromonospora exhibited versatile profiles. High metabolic diversity was recorded through the carbon substrate utilization profiles indicating that microbial communities are active participants in biogeochemical cycles in the deep sea. The most prominently utilized carbon substrates were α-cyclodextrin, glucose-1-phosphate, D-xylose, glycogen, and 2-hydroxy benzoic acid which serve as organic substrates for microbial metabolism, facilitating the decomposition of organic matter and, recycling carbon in deep-sea ecosystems. Multivariate statistical analyses confirmed that the environmental variables had a profound influence on the bacterial community. The findings shed light on spatial variability in the bacterial community structure, enzyme activity and metabolic profiles, and enhance our understanding of Bay of Bengal deep-sea sedimentary microbial ecology.

Soil Properties and Forest Decline in the North-Western Part of Romania

The paper presents the study of the soil quality and health expressed by the chemical and biological properties in a research field placed at Varciorog, Bihor County, Romania. The soil samples were collected from 3 soil variants in March 2023. In each soil variant, some soil chemical parameters and the abundance of bacteria were determined. The frequency and intensity of colonization, along with arbuscules and vesicles, were scored to determine the mycorrhizal potential of each soil. The community-level physiological profile was used to determine the functional microbiome and its ability to decompose a specific set of substrates. In the control variant (CTRL), which is a functional forest cultivated with beech in a proportion of 90%, the soil properties were compared with those determined from Site 1 (a declined mixed forest) and from Site 2 (chestnut forest in a stage of complete drying). The data were statistically processed with a one-way ANOVA test, followed by the Duncan post-hoc test, which revealed significant variation in the potential of microbial functional communities across the analyzed sites. Also, the soil parameters that significantly varied in the 3 soil variants were bacterial number, pH, humus, exchangeable aluminum, coarse sand, dust, and fine sand. The Pearson correlation was computed to study the links between bacterial numbers and chemical parameters. The results showed strong correlations between most of the studied soil properties. The Ecoplates approach to soil functional microbiome highlighted various differences between the microbial communities of the three tested sites. Mycorrhizal colonization shows different potentials for symbiosis formation. The peak of mycorrhizal colonization was in declined forest, with 43.36% colonization frequency and 24.56% intensity. Arbuscules reached 11.36% in declined forest, while in control and decayed sites, the indicator was under 4%. Vesicles are more associated with control and decayed forests, with values of presence over 1.30%. As an indicator of microbial general activity, the sum of recorded activities was higher in declined and decayed forests. At these sites, the activity of the functional microbiome was amplified. The decline process activates a higher diversity of functional groups and is associated with a larger area of substrate decomposition capacity, which indicates a more extensive range of microbial functions related to breaking down organic matter.

Some biological properties of the Kuidusun depression soils of Oymyakon

The aim of the study. To investigate some microbiological properties of the catenal series of soils in the Kuidusun depression of the Oymyakon Highlands. Location and time of the study. The study area is located in the vicinity of the Tomtor village (N63°15'41.94''; E143°10'26.91'') of the Oymyakonsky district of the Republic of Sakha (Yakutia, Russia). Soil samples were collected in the fall of 2011 at the main positions of the catena. The length of the catena is 38 km, the altitude a.s.l. is 727–821m. Soils are classified as Cambic Cryosols (fragic, мurshic), (forest); Skeletic Cryosols (aridic), (steppe meadow), Cambic Cryosols (fluvic), (typical meadow); Folic Cryosols (swampy meadow). Methods. The content of labile soil organic matter (LOC) was determined photocalorimetrically in soil extracts with phosphate buffer (1/15 M, pH 6,8). The number of colony-forming units (CFU) was determined using standard MPA, KAA, and Czapek media. The functional spectrum of the soil microbiota was assessed using the community level physiological profile (CLPP) method. All properties were studied in 10 cm thick layers to a depth of 40 cm. Soil urease activity was assessed by ammonium production from urea. Results. At the time of sampling moisture content of soil samples down the catena increased from 5 to 20%, whereas the LOC content increased from 2 to 6 g C /kg. In the 0–10 cm layer, the greatest accumulation of LOC was observed in the soil under a typical meadow. The highest number of CFU (150 million/g soil) in a dilute MPA medium was also found there. An increase in the proportion of CFU in the dormant state was revealed in the soil series from the lower position of the catena to the upper one. In the same series, an increase in the oligotrophic index of the community was noted. The highest metabolic activity was observed in the soil under a swampy meadow, whereas the lowest was shown by the soil under a forest. The enrichment of soil organic matter with microbiota cells increased in the series of soils f in the following order: a swampy meadow – a typical meadow – a steppe meadow, whereas the specific activity of the microbiota decreased. Urease activity of the soil was detected mainly in the 0–10 cm layer; in the underlying layers the activity was more than 500 times lower. Conclusions. The biological properties of the studied soils corresponded to the known patterns established for the catenal series of soils in other soil and climatic conditions. The peculiarity of the studied soils was related to the extremely sharp differentiation of the microbiological profile. The absolute predominance of actinomycetes CFU in the soil under the steppe meadow was the major characteristic feature of the culturable part of the soil microbial community.

Dry–wet cycles induce the decoupling of carbon and nitrogen mineralization at high temperatures in semi-arid grassland soil

Soil carbon (C) and nitrogen (N) transformations are typically interlinked because of the conserved elemental stoichiometry of microbes, which can be remarkably altered by intensified temperature variations and dry–wet (DW) cycles. However, the interactive effects of temperature and DW cycles on soil C and N transformations and how microbial communities mediate these processes remain largely unknown. In this study, we subjected a semi-arid grassland soil from northern China to four successive DW cycles at 15, 25, and 35 °C. The soil respiratory rates during incubation, labile C and N fractions, activities of C and N acquisition enzymes, community-level physiological profiles, and microbial community composition at the end of the incubation were determined. Soil respiration rates decreased with drying but sharply increased with wetting, particularly at higher temperatures. Soil DW cycles did not significantly affect cumulative C mineralization and net N mineralization at 15 °C. However, they decreased cumulative C mineralization by 24.5% and 23.4% and increased net N mineralization by 48.6% and 41.7% at 25 and 35 °C, respectively, indicating a decoupling of C and N mineralization at higher temperatures. As the temperature increased, soil DW cycles decreased cellobiohydrolase and peroxidase activities and the microbial use of amino acids and lipids but increased N-acetyl-β-glucosaminidase activities and the microbial use of saccharide polymers and recalcitrant amines. Moreover, soil DW cycles increased the abundances of gram-positive bacteria and actinomycetes and gram-positive-to-gram-negative bacteria ratios with increasing temperature, particularly at 35 °C. Overall, our findings suggest that DW cycles at higher temperatures decelerated the mineralization of organic soil C by decreasing cellobiohydrolase and peroxidase activities. However, DW cycles at higher temperatures improved N mineralization by shaping the microbial communities to excrete more recalcitrant-organic-N acquisition enzymes, thereby meeting their high N requirements.

Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing.

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.

Sustainable Restoration of Soil Functionality in PTE-Affected Environments: Biochar Impact on Soil Chemistry, Microbiology, Biochemistry, and Plant Growth

Biochar can be useful for the functional recovery of soils contaminated with potentially toxic elements (PTEs), even if its effectiveness is variable and sometimes limited, and conflicting results have been recently reported. To shed some light on this regard, softwood-derived biochar was added at 2.5 (2.5-Bio) and 5.0% w/w (5.0-Bio) rates to an acidic (pH 5.74) soil contaminated by Cd (28 mg kg−1), Pb (10,625 mg kg−1), and Zn (3407 mg kg−1). Biochar addition increased soil pH, available P and CEC, and reduced labile Cd, Pb, and Zn (e.g., by 27, 37, and 46% in 5.0-Bio vs. the unamended soil). The addition of biochar did not change the number of total heterotrophic bacteria, actinomycetes, and fungi, while it reduced the number of Pseudomonas spp. and soil microbial biomass. Dehydrogenase activity was reduced in amended soils (e.g., by ~60 and 75% in 2.5- and 5.0-Bio, respectively), while in the same soils, urease increased by 48 and 78%. Approximately 16S rRNA gene amplicon sequencing and the Biolog community-level physiological profile highlighted a significant biochar impact (especially at a 5% rate) on soil bacterial diversity. Tomato (but not triticale) yield increased in the amended soils, especially in 2.5-Bio. This biochar rate was also the most effective at reducing Cd and Pb concentrations in shoots. Overall, these results demonstrate that 2.5% (but not 5.0%) biochar can be useful to restore the soil chemical fertility of PTE-polluted soils with limited (or null) impact on soil microbial and biochemical parameters.

Soil management effects on soil organic matter properties and carbon sequestration (SOMPACS)

SOMPACS is a project recommended by EJP SOIL for funding under the 1st External Call "Towards Healthy, Resilient and Sustainable Agricultural Soils". The goal of this project is to assess management practices that enrich organic matter pools that are resilient to rapid microbial decomposition. The project started in 2022 as a consortium of 12 research institutions from Poland, Germany, Ireland, Lithuania, UK, Italy and USA for a period of three years. Soil and vegetation samples from eight long-term experiments that differ in soil management practices (i.e., conventional vs. no-tillage; mineral vs. organic fertilization; with and without catch crop; and arable land vs. undisturbed grassland) are investigated. Study sites include: 22- and 54-year long experiments in Lithuania; 26-year long experiment in Italy; 30- and 40-year long experiments in Ireland; 30- and 46- and 100-year long experiments in Poland; and 178-year long Broadbalk experiment in Great Britain. Additional experimentation includes assessing the impact of root growth promoting amendments (commercially available humic substances, biochar and biogas digestate) on stable organic matter pools. In parallel with soil sampling, plant productivity are measured in all field experiments. This investigation is couples fields studies with small-scale experimental plots and laboratory incubations under controlled conditions. In addition to assessing basic soil properties, the following state-of-the-art analyses are conducted: SOM composition and stability by Py-GC-MS; fractionation of aggregate size classes and C pools of increasing physicochemical protection; isotopic analysis of δ13C and δ15N performed on different SOM pools; microbiological properties (community-level physiological profiling, selected functional genes involved in C and N cycles, microbiome and mycobiome analyses by next-generation sequencing, genetic diversity using terminal restriction fragment length polymorphism); enzymatic activity; soil water retention and soil water repellency; mineral composition of clay fraction; (8) soil structure stability. SOM composition and stability by Py-GC-MS; fractionation of aggregate size classes and C pools of increasing physicochemical protection; isotopic analysis of δ13C and δ15N performed on different SOM pools; microbiological properties (community-level physiological profiling, selected functional genes involved in C and N cycles, microbiome and mycobiome analyses by next-generation sequencing, genetic diversity using terminal restriction fragment length polymorphism); enzymatic activity; soil water retention and soil water repellency; mineral composition of clay fraction; (8) soil structure stability. The most resistant SOM pool (humin) are isolated by different methods (isolation vs. extraction) and examined for chemical composition and structure, using spectrometric and spectroscopic techniques (mass spectrometry, NMR, FTIR, EPR, UV-Vis-NIR, fluorescence). The carbon stocks in the soil profile will be evaluated and the carbon extractable in cold water will be determined to assess the potential carbon leaching and microbial availability. Additionally, in-field soil carbon dioxide (CO2) fluxes from selected experiments is monitored. Thus far, soil samples (0-100 cm depth) were collected and the humin fraction from surface A horizon was isolated for spectroscopic studies. Crop yield and vegetation productivity was also assessed. The research was financed by NCBR (EJPSOIL/I/78/SOMPACS/2022).

Quantifying the Respiratory Pattern of Rhizosphere Microbial Communities in Healthy and Diseased Tomato Plants Using Carbon Substrates

The sustainable production of tomatoes (Solanum lycopersicum) is important, and this can be achieved by determining the rate of respiration of microbes in the tomato plants' rhizosphere soil. This study aimed at the potential of microbes to utilize carbon substrates embedded in the rhizosphere soil thereby contributing to the healthy nature of the tomato plants. The potential soil physiochemical features and utilization of carbon substrate by soil microorganisms as a result of their respiration to reveal their functions in the ecosystem were evaluated. The soil samples were amassed from the healthy tomato plant rhizosphere, diseased tomatoes, and bulk soil in this study. The physiochemical features and carbon substrate utilization in the bulk soil samples, and rhizosphere samples of powdery diseased, and healthy tomato plants were assessed. The MicroRespTM procedure was used to determine the community-level physiological profiles (CLPP) employing fifteen (15) carbon (C) substrates selected based on their importance to microbial communities embedded in the soil samples. Our results revealed that various physiochemical properties, moisture content, water retention, and C substrates including sugar, amino acid, and carboxylic acid were greater in HR and the substrates were not significantly different (p < 0.05). The study reveals higher soil respiration in HR as a result of the microbial communities inhabiting HR utilizing more of the C-substrates. This investigation contributes to the tomato plant's healthy state as the microbial communities utilized carbon substrate compared to DR after employing the CLPP assays.

Soil biological activity after a sixty-year fertilization practice in a wheat-maize crop rotation.

This study aimed to survey the long-term effects of fertilization practices on the functional diversity of the soil microbiota. A 60-year fertilization experiment with mineral fertilizers, farmyard manure and combined treatments was sampled in two consecutive years in maize (Zea mays L.) and wheat (Triticum aestivum L.). Soil chemical properties, plant growth and physiological parameters were measured. The MicroRespTM method was applied to assess the community level physiological profiles (CLPPs) of the rhizosphere soil, and the arbuscular mycorrhizal fungal (AMF) colonization of the roots was determined. Samples were taken in the early vegetative stages, at flowering, and at harvest in both years. The measured parameters were analysed using multifactorial ANOVA to determine treatment effects, crop-dependent differences, and seasonality. PCA analysis was performed on the data matrix to reveal more complex correspondences, and Pearson's product-moment correlation was used to confirm relationships between some of the measured soil and plant parameters. Fertilization treatments caused long-term changes in some biological parameters such as: MicroRespTM parameters, citrate utilization, total substrate-induced respiration value, and the ratio of utilization of amino acids and sugars. The rate of AMF colonization responded mainly to the plant nutrition status and the plant requirements, suggesting a plant-mediated effect in the case of mycorrhiza. Mineral nitrogen fertilization and soil acidification were found to be the main factors affecting the catabolic activity of soil microbiota, while AMF colonization responded to the balance of plant nutrition.

Vermicast Analysis with the Earthworm Species Pheretima losbanosensis (Crassiclitellata: Megascolecidae): Bacterial Profiles for Potential Applications in Agriculture

In the Philippines, the use of non-native earthworm species in vermicomposting is popular. Given that the country is a vital geographical resource for earthworm diversity, the study of earthworm species to establish the potential of their vermicasts in agricultural applications is essential. In this study, the bacteria associated with the vermicasts of the recently described indigenous species, Pheretima losbanosensis, were investigated using next-generation sequencing, community-level physiological profiling, and NPK activity screening. The results showed diverse bacterial species belonging to the phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Spirochaetes, Thermodesulfobacteria, and Verrucomicrobia. Higher diversity and carbon substrate utilization (p &lt; 0.05) of amines and amides, phenolic compounds, polymers, and carboxylic and acetic acids were exhibited by the bacterial communities of P. losbanosensis compared to those of Eudrilus eugeniae. Likewise, bacteria (n = 25) isolated from P. losbanosensis vermicasts had higher nitrogen fixation and phosphate and potassium solubilization activities (p &lt; 0.05) than the bacteria (n = 20) isolated from E. eugeniae vermicasts. Overall, our results indicate that the diverse bacterial communities inhabiting the vermicasts of P. losbanosensis have nutrient mineralization and carbon substrate utilization activities that may have applications in sustainable agriculture as a potential organic input to promote plant growth and improve soil substrate.

Microbially modified effect of exogenous organic matter on soil chemical and biological indices and plant responses

PurposeExogenous Organic Matter (EOM) enriches and regenerates the soil, while solving the problem of landfilling waste such as sewage sludge and bottom sediments. The main purpose of the presented study was to estimate the influence of type and dosage of applied EOM on soil biological characteristics and supporting plant growth, with consideration of inoculation with PGPR (plant growth-promoting rhizobacteria).Materials and methodsThe soil samples were characterized by measuring key enzyme activities, determining the community-level physiological profiling (CLPP) using Biolog EcoPlates, abundance of microorganisms and evaluation physical and chemical properties.Results and discussionApplication of EOM mostly increased enzyme activity as well as overall metabolic activity compared to control sample. Increasing the dose of poultry manure and sewage sludge from 20 to 40 t ha−1 increased dehydrogenase, acid and alkaline phosphatase activity. Moreover, the addition of EOM affected the metabolic activity and the number of selected groups of bacteria and fungi.ConclusionsIn the research it was proven that application of EOM leads to relatively rapid and positive changes in soil biological activity. The research also confirmed that the supporting factor for plant growth was the inoculation with PGPR bacteria. This approach, together with the reuse of organic wastes may become an attractive approach in sustainable cropping systems in a circular economy system.Graphical

Changes in Soil Nematode and Microbial Community in Cucumber Root-Zone Soil Shaped by Intercropping with Amaranth

Intercropping systems often contribute to soil health management including inhibiting root-knot nematode disease. The main purpose of this study was to investigate the potential effect of the cucumber-amaranth intercropping system on soil biota, specifically the nematode and microbial communities. Furthermore, the cucumber root-nematode disease was also evaluated. The study found significant effects of cultivation systems (cucumber-amaranth intercropping and cucumber monocropping) and growing seasons (winter-spring (WS) and autumn-winter (AW)) on both soil nematode and microbial community structures in cucumber root-zone soil. Intercropping resulted in a decrease in the relative abundance of Meloidogyne spp., which was consistent with the observed alleviation of root-knot nematode disease. Bacterivorous nematodes were dominant in the intercropping system. The microbial biomass and community-level physiological profiles (CLPP) were generally higher in the intercropping system. Beta diversity analysis showed that the composition of microbial communities varied widely among the treatments and growth seasons. These findings suggest that intercropping with amaranth can regulate soil biota, leading to decreased incidence of root-knot nematodes (RKNs) diseases.

Dissipation of pesticides by stream biofilms is influenced by hydrological histories.

To evaluate the effects of hydrological variability on pesticide dissipation capacity by stream biofilms, we conducted a microcosm study. We exposed biofilms to short and frequent droughts (daily frequency), long and less frequent droughts (weekly frequency) and permanently immersed controls, prior to test their capacities to dissipate a cocktail of pesticides composed of tebuconazole, terbuthylazine, imidacloprid, glyphosate and its metabolite aminomethylphosphonic acid. A range of structural and functional descriptors of biofilms (algal and bacterial biomass, extracellular polymeric matrix (EPS) concentration, microbial respiration, phosphorus uptake and community-level physiological profiles) were measured to assess drought effects. In addition, various parameters were measured to characterise the dynamics of pesticide dissipation by biofilms in the different hydrological treatments (% dissipation, peak asymmetry, bioconcentration factor, among others). Results showed higher pesticide dissipation rates in biofilms exposed to short and frequent droughts, despite of their lower biomass and EPS concentration, compared to biofilms in immersed controls or exposed to long and less frequent droughts. High accumulation of hydrophobic pesticides (tebuconazole and terbuthylazine) was measured in biofilms despite the short exposure time (few minutes) in our open-flow microcosm approach. This research demonstrated the stream biofilms capacity to adsorb hydrophobic pesticides even in stressed drought environments.