Microbial Metabolic Diversity Research Articles

Effects of plastic film mulching on soil microbial carbon metabolic activity and functional diversity at different maize growth stages in cool, semi-arid regions

IntroductionPlastic film mulching has been widely used to enhance soil hydrothermal conditions and increase crop yields in cool, semi-arid areas. However, its impact on soil microbial carbon metabolic activity and functional diversity during plant growth remains unclear despite their important roles in nutrient cycling and soil quality evaluation.MethodsThis study used the Biolog EcoPlate technique to investigate the dynamics and driving factors of soil microbial carbon metabolic activity and functional diversity at different maize growth stages following plastic film mulching.Results and discussionThe results revealed that film mulching significantly increased microbial carbon metabolic activities [represented by average well color development (AWCD)] by 300% at the seedling stage and by 26.8% at maturity but decreased it by 47.4% at the flowering stage compared to the control (without mulching). A similar trend was observed for the microbial functional diversity index. Redundancy analysis identified soil moisture (SM), soil temperature (ST), dissolved organic carbon (DOC), microbial biomass carbon (MBC), and bacteria amounts as the primary factors influencing changes in soil microbial carbon source utilization. The mulch treatment significantly increased SM at all growth stages, while its warming effect disappeared at the flowering stage. Soil DOC, MBC, and bacterial populations were notably higher under mulching at the seedling and maturity stages but lower at the flowering stage. Pearson correlation analysis showed that changes in SM, ST, DOC, MBC, and bacterial populations positively correlated with the utilization of all carbon source classes, AWCD, and functional diversity indexes after film mulching. Furthermore, maize grain yield and water use efficiency increased by 142 and 129%, respectively, following film mulching. In conclusion, plastic film mulching enhanced soil microbial carbon metabolic activity and functional diversity at the seedling and maturity stages, improving crop yields in cool, semi-arid areas. Furthermore, the decrease in soil carbon metabolic capacity at flowering stage highlights that supplementing soil carbon sources should be considered after continuous film mulching to sustain or enhance farmland productivity and soil quality.

Beneath the apple trees - Exploring soil microbial properties under Malus domestica concerning various land management practices

The presented study evaluated the impact of six land management practices on soil bacterial and fungal communities under apple trees: green field belts, forests, gardens with trees and ornamental plants, gardens with farm animals, and uncultivated and cultivated orchards. The study explored soil microbial properties including the enzymatic activity of dehydrogenases (tested by colorimetric reaction with 2,3,5-triphenyl-tetrazolium chloride), metabolic profile (using Biolog™ ECO Plates), metataxonomy structure (Next Generation Sequencing using Illumina®), followed by physicochemical properties (pH, N, P, K, microelements concentrations, organic matter, and Corg content). The hypothesis was that different land management practices would influence soil microbial properties, with cultivated orchards expected to show significantly lower dehydrogenases activity, and higher substrate-based respiratory than biomass response, within substrate stress occurrence, when testing metabolic profiles, but also different composition and lower relative abundances of specific microbial taxa and different biomarker genera, compared to other treatments. We aimed to identify practices promoting diverse microbial substrate-based metabolic and taxa diversity responses, with a focus on Bacillus and Trichoderma abundances, which are potential biological agents against fungal pathogens. As expected the presented research revealed significant statistical variations in microbial communities among different land management practices in soil beneath apple trees. It was accordingly noted that cultivated orchards, but also green belts, clearly exhibited reduced microbial activity (3.59 and 4.76 TPF kg−1 d−1, respectively) compared to gardens and uncultivated orchards (12.08 and 9.89 TPF kg−1 d−1). Cultivated orchards notably showed higher respiration levels and substrate stress compared, especially to forests and other land management practices represented by a clear separation of observed according to Sneath's criteria in cluster analysis. Different land management practices induce unique stress responses in microbial communities: forests struggled with B-Methyl-d-Glucoside, gardens with Serine and Putrescine, cultivated orchards with d-Glucosaminic Acid and Cyclodextrin, and bounds with 2-Hydroxy-Benzoic Acid. Substantial differences were also observed in the relative abundance of the top ten bacterial and fungal orders, and biomarker genera representatives. In cultivated orchards, there was a significant decrease in the relative abundance of many bacterial taxa such as e.g. Rhizobiales, Burkholderiales, Vivinamibacterales, and fungal taxa including Eurotiales, and Saccharomycetales. Notably, no significant differences were noted for Bacillus abundance among tested management practices. Forests favored Trichoderma abundance the most among tested practices (relative abundance 0.05 %). In turn, Trichoderma representatives were revealed as biomarker genera in gardens with animals. Williamsia representatives, as found in uncultivated orchards were suggested to be a biomarker of less disturbance, resulting from area restoration. Overall, the study discussed how different land management practices influence soil microbial communities and their functional roles, emphasizing the potential impacts of use on soil health and biodiversity within its implications. The most important recommendation bullet points:•using Williamsia representatives as a soil biomarker microorganism to indicate successful area restoration processes in apple orchards,•using d-Glucosaminic Acid metabolic stress test to reveal early difficulties in controlling fungal pathogens in soil microbial communities,•promoting diverse plant covers and reasonably reduced agrochemical inputs in apple orchards for enhancing soil microbial resilience,•preserving habitats of wild apple trees in forests or green belts, as these environments exhibit reduced metabolic stress and support the occurrence of fungi like Trichoderma, in the context of locations from which such isolates should be sought for further biocontrol use.

Unveiling the Impact of Soil Prebiotics on Rhizospheric Microbial Functionality in Zea mays L.

Prebiotics, a subset of biostimulants, have garnered attention for their potential to enhance soil conditions and promote plant growth, offering a promising alternative to conventional agricultural inputs. This study explores how two commercial prebiotics, K1® and NUTRIGEO L® (SPK and SPN), impact soil functions compared to a control (SP). The experiment involved agricultural soil amended with organic wheat straws and cultivated with Zea mays L. Previous research demonstrated substantial effects of these prebiotics on plant biomass, soil parameters, and microbial community ten weeks after application. The present study delves deeper, focusing on soil microbial abundance, enzyme activities, and metabolic diversity. Analysis revealed that SPN notably increased the fungi-to-bacteria ratio, and both prebiotics elevated the activity of several key enzymes. SPN enhanced α-glucosidase and β-galactosidase activities, while SPK increased arylsulfatase, phosphatase, alkaline phosphatase, and urease activities. Enzymatic indexes confirmed the positive impact on soil functional diversity and fertility. Additionally, prebiotic treatments showed distinct metabolic profiles, with SPK degrading eleven carbon sources more rapidly across five groups and SPN accelerating the decomposition rate of four carbon sources from three groups. These findings highlight the ability of prebiotics to shape microbial communities and enhance soil fertility by modulating their functional activity and diversity.

Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China

Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.

Context dependence of warming‐induced shifts in montane soil microbial functions

Abstract High elevation and latitude ecosystems are experiencing high levels of anthropogenic atmospheric warming. Climate warming may directly change soil microbial activity and alter ecosystem carbon dynamics and productivity, but increasing evidence suggests these responses may depend on other biotic factors such as plant community composition and abiotic factors such as moisture. We examined how abiotic (warming) and biotic (presence of dominant plant species) factors interact to affect soil microbial processes. Our experiment deployed the independent and combined treatments of experimental warming and dominant plant species removal in a high and low elevation montane meadows. We analysed multiple soil microbial responses to warming and the presence of a dominant plant at three times throughout the growing season, including soil respiration, microbial metabolic functional diversity, microbial biomass carbon and nitrogen, and extracellular enzyme potential activity. Overall, there were few independent microbial responses to either the warming or the removal treatments. There was a significant interaction between warming and the removal of a dominant plant species, where microbial biomass and the activity of some microbial enzymes were lower in warmed plots where the dominant species was removed relative to control plots. The effect of warming on extracellular enzyme activity was typically observed only at the high‐elevation site. In contrast, we found that effects of warming were consistent across the growing season, despite strong temporal variation in microbial properties. Our results emphasize the need to further consider soil microbial responses to warming under multiple environments, including shifts in both biotic and abiotic factors, to aid in predictions of carbon dynamics under future global change. Read the free Plain Language Summary for this article on the Journal blog.

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

Endophyte inoculation enhanced microbial metabolic function in the rhizosphere benefiting cadmium phytoremediation by Phytolaccaacinosa

Microbial metabolic activities in rhizosphere soil play a critical role in plant nutrient utilization and metal availability. However, its specific characteristics and influence on endophyte assisted phytoremediation remains unclear. In this study, an endophyte strain Bacillus paramycoides (B. paramycoides) was inoculated in the rhizosphere of Phytolacca acinosa (P. acinosa), and microbial metabolic characteristics of rhizosphere soils were analyzed using Biolog system to investigate how they influence phytoremediation performance of different types of cadmium contaminated soil. The results indicated that endophyte B. paramycoides inoculation enhanced bioavailable Cd percentage by 9–32%, resulting in the increased Cd uptake (32–40%) by P. acinosa. With endophyte inoculation, the utilization of carbon sources was significantly promoted by 4–43% and the microbial metabolic functional diversity increased by 0.4–36.8%. Especially, B. paramycoides enhanced the utilization of recalcitrant substrates carboxyl acids, phenolic compounds and polymers by 48.3–225.6%, 42.4–65.8% and 15.6–25.1%, respectively. Further, the microbial metabolic activities were significant correlated with rhizosphere soil microecology properties and impact phytoremediation performance. This study provided new insight into the microbial processes during endophyte assisted phytoremediation.

Deciphering the Impact of Induced Drought in Agriculture Soils: Changes in Microbial Community Structure, Enzymatic and Metabolic Diversity

Prolonged drought stress may have a significant impact on the structure and activity of the soil microbial community. Our study aims to investigate the impact of short-term drought (2 months) on the microbial community structure, enzymes, and metabolic diversity in four agricultural soils (Gniewkowo (G), Lulkowo (L), Wielka Nieszawka (N) and Suchatówka (S) sites) in Poland. These four types of soil were selected based on differences in their texture (gleyic luvisol Phaeozem in G (rich in clay and humus), stagnic luvisol in L, fluvisol in N and haplic luvisol in S (sandy)). We investigated the (1) number of bacteria, actinomycetes (formally phylum Actinomycetota) and fungi; (2) microbial community (16S rRNA and ITS amplicon regions); (3) biological activity by community-level physiological profiling (CLPP); (4) soil enzyme activities (dehydrogenases (DH), phosphatases (acid ACP and alkaline ALP) and urease (UR)); and (5) soil chemical properties. At the end of our experiment, we observed a significant decrease in soil moisture content with the highest in the soil from the S site. Overall, there was no change in total bacteria, but actinomycetes and fungal numbers increased after the 1st week with a decrease in moisture content. ACP activity decreased in three out of four analyzed soil samples. The exception was in sample G, where activity increased for 1–2 weeks and then decreased. ALP activity significantly increased with a decrease in moisture in the 1st week and was lowest at the end of the experiment. DH activity increased up to the 4th week in the G and N samples and up to the 2nd week in the L and S samples. UR activity showed variations in the analyzed samples. A reduction in the utilization of carbon sources (except D-mannitol and L-asparagine) was noted with the highest reduction in the G sample followed by the L, N and S samples. Thus, the pattern of changes was different depending on the analyzed soil type. The 16S rRNA and ITS amplicon sequencing revealed a decrease in the relative abundance of Pseudomonadota, Basidiomycota, Apicomplexa, and increased abundance of Actinomycetota, Bacillota and Ascomycota under prolonged drought conditions. With this, we concluded that drought conditions resulted in a significant alteration of soil microbial communities, enzyme activities, and metabolic diversity in the investigated soils.

Vinasse as a substrate for inoculant culture and soil fertigation: Advancing the circular and green economy

Vinasse is a by-product with a key role in circular economy. In this work, we analyze sugarcane vinasse as culture medium for obtaining single and mixed inoculants. Trichoderma harzianum MT2 was cultured in single and sequential co-culture with Pseudomonas capeferrum WCS358 or Rhizobium sp. N21.2. Fungal biomass in single culture was more than three folds higher in vinasse than in a standard medium, and was higher in co-culture with Rhizobium sp. N21.2 than with P. capeferrum WCS358. Bacterial growths in vinasse, in particular P. capeferrum WCS358, were improved in co-culture with T. harzianum MT2. Residual vinasses, obtained after microbial growth, presented almost neutral pH and lower conductivities and toxicity than raw vinasse. Fertigation with residual vinasses modifies characteristics of soil evidenced in the total N, cation exchange capacity, urease and acid phosphatase, and microbial metabolic diversity, in comparison to raw vinasse. In general, soil fertigation with residual vinasse from co-culture with P. capeferrum WCS358 is more similar to irrigation with water. Treatment evaluation indicates that vinasse is suitable for the production of mixed inoculants containing T. harzianum. The co-culture with P. capeferrum WCS358 improves the characteristics of the residual vinasse allowing a fertigation with less detrimental effect in soil in comparison to Rhizobium sp. N21.2. Obtaining valuable biomass of single or mixed inoculants in vinasse with lower ecological impact is relevant for the circular and green economy.

Application of the Biolog EcoPlate™ technique for assessing the microbial metabolic diversity in moss profiles of continental Antarctica

Little is known about metabolic capabilities of microbial assemblages in continental Antarctic to utilize diverse carbon sources within moss profiles consisting of live, senescent, and dead moss tissues in different stages of decomposition. In the present study, microbial metabolic diversity was determined using Biolog EcoPlate™ for samples of Bryum pseudotriquetrum/B. archangelicum complex collected at five sites located in coastal outcrops of the Lützow-Holm Bay area (Queen Maud Land), East continental Antarctica, and effects of chemical, biological, and physical properties of the moss tissues were explored. The average well-color development, the number of substrates utilized, Simpson's diversity index and equitability of the microbial substrate utilization, and the utilization of carbohydrates, amino acids/amines, carboxylic acids, and polymers varied significantly among the five sites and among four layers of moss profiles. Principal component analysis showed that the utilization of L-asparagine, L-arginine, D-galacturonic acid, Tween 40, Tween 80, and D-mannitol mainly contributed to the variance in the microbial metabolic diversity between sites and moss profiles. The linear mixed models indicated that the relative content of recalcitrant organic components, the number of fungal species, and the water content of moss tissues affected the diversity of microbial utilization of carbon sources.

Straw addition increases enzyme activities and microbial carbon metabolism activities in bauxite residue

Recovery of microbial functions is one of the critical processes in the nutrient cycling of bauxite residue for improving revegetation. Straw is considered to be effective to increase microbial diversity and drive the development of the microbial community, but its effect on microbial carbon metabolism has not been illustrated. The present study evaluated the effects of phosphogypsum (PG), straw (SF) and phosphogypsum plus straw (PGSF) on physicochemical properties, enzyme activities, and microbial carbon metabolism activities in bauxite residue. After 180 days incubation, PG, SF and PGSF treatment significantly reduced the residue pH from 10.85 to 8.64, 9.39 and 8.06, respectively. Compared to CK treatment, SF treatment significantly increased the content of total organic carbon (TOC) and organic carbon fractions (DOC, MBC, EOC, and POC). In addition, straw addition significantly increased glucosidase, cellulose, urease, and alkaline phosphatase by 7.2-9.1 times, 5.8-7.1 times, 11.1-12.5 times, and 1.1-2.2 times, respectively. The Biolog results showed that straw addition significantly increased microbial metabolic activity (AWCD) and diversity in bauxite residue. Redundancy analysis indicated total nitrogen (TN) and carbon fractions (POC, MBC and DOC) were the most important environmental factors affecting microbial metabolic activity and diversity in bauxite residue. These findings provided us with a biogeochemical perspective to reveal soil formation in bauxite residue and suggested that nutrient supplement and regulation of salinity-alkalinity benefit the establishment of microbial communities and functions in bauxite residue.

Spatial variation and metabolic diversity of microbial communities in the surface sediments of the Mariana Trench.

Mariana Trench represents the deepest and one of least explored biosphere on Earth, and its carbon sources include euphotic sinking, lateral transportation and diffusion from underlying crust, etc. By far the spatial variation of microbial community with associated organic carbon degradation potential in the surface sediments of the Mariana Trench were still largely unknown. Based on the high-throughput 16S rRNA amplicon sequencing, significantly different microbial community structure was overserved between the shallow (<10,000 m) and deep stations (>10,000 m), which could be explained by spatial variation of Chloroflexi, Proteobacteria and Crenarchaeota, with sampling depth and total organic carbon (TOC) content as the environmental driving forces. During the 109-day incubation with Biolog EcoPlate™ microplate, polymers and carbohydrates were preferentially used, followed by amino acids and carboxylic acids, and microbial metabolic diversity was significantly different between the shallow and deep stations. The metabolic diversity of microorganisms at most shallow stations was significantly lower than that at deep stations. This could potentially be attributed the metabolic capabilities of different microbial groups with varied ecological niches, and reflected the initial preference of carbon source by the nature microbes as well. Our study obtained a rough assessment of physiological and taxonomic characteristics of the trench sediment microbial community with polyphasic approaches. Distinct microbial structure and potential carbon metabolic functions in different sampling depths might led to the differentiation of ecological niches, which enable various microorganisms to make full use of the limited resources in the deep sea, and provided a research basis for further exploration of the carbon cycle in different deep-sea regions.

Redox conditions and a moderate anthropogenic impairment of groundwater quality reflected on the microbial functional traits in a volcanic aquifer

Groundwater is an important freshwater resource and hosts specialized microbial assemblages providing fundamental ecosystem services. The current knowledge on the role of aquatic microorganisms in subsurface ecosystems is still limited. This work aimed to explore the links between groundwater hydrogeochemical properties and microbial community traits in a volcanic unconfined aquifer, moderately impacted by anthropic activities. The main physical and chemical parameters of groundwater samples were analyzed, along with microbial biomass (total cell counts, ATP-active biomass concentration), potential metabolic activity, and physiological profiles at the microbial community level (Biolog ™ EcoPlates). The results showed the coexistence of oxidizing and reducing groundwater conditions across the study area. We discriminated two groups of oxidizing/reducing groundwater samples (Ox and Red), each including two subgroups with different chemical conditions attributed to contrasting levels of anthropogenic impact for non-intensive agricultural practices and waste disposal activities (Ox − and Ox + ; Red − and Red +). Although the microbial biomass was likely not affected by changing redox, the microbial metabolic potential and functional diversity changed significantly. In the Ox samples, the community-level physiological profiles were different, mainly owing to the utilization of carboxylic acids (Ox − > Ox +) and carbohydrates (Ox + > Ox −). In the Red samples, a wider set of organic substrates were consumed by the microbial communities, including those less bioavailable (e.g., phenols). Significant differences were also found between Red − and Red + , mainly owing to the relative increase in the utilization of amino acids in Red − , polymers and amines in Red + , along with the active biomass. By reflecting the local redox conditions and moderate levels of anthropogenic impact, the applied approach highlighted changes of microbial metabolic potential and physiological profiles that imply direct repercussions on biogeochemical cycling and the ecosystem services provided by groundwater microorganisms.

Assessing Microbial Metabolic and Biological Diversity to Inform Natural Product Library Assembly.

The pressing need for novel chemical matter to support bioactive compound discovery has led natural product researchers to explore a wide range of source organisms and environments. One of the implicit guiding principles behind those efforts is the notion that sampling different environments is critical to accessing unique natural products. This idea was tested by comparing fungi from disparate biomes: aquatic sediments from Lake Michigan (USA) and terrestrial samples taken from the surrounding soils. Matched sets of Penicillium brevicompactum, Penicillium expansum, and Penicillium oxalicum from the two source environments were compared, revealing modest differences in physiological performance and chemical output. Analysis of LC-MS/MS-derived molecular feature data showed no source-dependent differences in chemical richness. High levels of scaffold homogeneity were also observed with 78-83% of scaffolds shared among the terrestrial and aquatic Penicillium spp. isolates. A comparison of the culturable fungi from the two biomes indicated that certain genera were more strongly associated with aquatic sediments (e.g., Trichoderma, Pseudeurotium, Cladosporium, and Preussia) versus the surrounding terrestrial environment (e.g., Fusarium, Pseudogymnoascus, Humicola, and Acremonium). Taken together, these results suggest that focusing efforts on sampling the microbial resources that are unique to an environment may have a more pronounced effect on enhancing the sought-after natural product diversity needed for chemical discovery and screening collections.

Insights into Bacterial Community Structure and Metabolic Diversity of Mercury-Contaminated Sediments from Hyeongsan River, Pohang, South Korea.

This study investigated the bacterial community structure and metabolic diversity and their relationship with Hg and other environmental variables in sediments collected from different locations (HSR-1-HSR-6) in the Hyeongsan River estuary in South Korea. The results showed that the highest total mercury (THg) and methylmercury (MeHg) concentrations were in HSR-2, with values of 4585.3µg/kg and 13.4µg/kg, respectively. The lowest THg (31.9µg/kg) and MeHg (0.1µg/kg) concentrations were found in HSR-1. Sulfate and organic matter (OM) were more influential environmental variables, revealing a positive association with THg and MeHg and negatively affecting bacterial and metabolic diversities. Bacterial and metabolic diversities were also negatively impacted by the THg and MeHg concentrations. Proteobacteria and Bacteroidetes were abundantly distributed in all the sediments. The dominance of Proteobacteria was upscaled in all the heavily Hg-contaminated sites (HSR-2-HSR-6), and it was the only phylum that showed a significant positive correlation with THg, MeHg, and OM. The genera Sulfurovum and Sulfurimonas were abundantly observed in sites with high Hg contamination, whereas Congregibacter, Gaetbulibacter, Ilumatobacter, Methylotenera, Nevskia, and Sediminibacter were only detected in low Hg-contaminated sites (HSR-1). The community-level physiological profile data showed the highest (1.0) average well color development (AWCD) value in HSR-1 and the lowest (0.45) AWCD value in HSR-2. Overall, these results demonstrated the inhibitory effects of THg, MeHg, and other environmental variables on microbial communities and metabolic diversity. These findings broaden the current knowledge on the dynamics of bacterial and metabolic diversities in Hg-contaminated sediments and might be useful in the management of Hg pollution.

Exogenous Microorganisms Promote Moss Biocrust Growth by Regulating the Microbial Metabolic Pathway in Artificial Laboratory Cultivation.

Moss-dominated biocrusts (moss crusts) are a feasible approach for the ecological restoration of drylands, but difficulty obtaining inoculum severely limits the progress of large-scale field applications. Exogenous microorganisms could improve moss growth and be conducive to moss inoculum propagation. In this study, we investigated the growth-promoting effects and potential mechanisms of exogenous microorganism additives on moss crusts. We used an incubator study to examine the effects of inoculation by heterotrophic microorganisms (Streptomyces pactum, Bacillus megaterium) and autotrophic microorganisms (Chlorella vulgaris, Microcoleus vaginatus) combined with Artemisia sphaerocephala gum on the growth of Bryum argenteum, the dominant moss crusts species in sandy deserts. Amplicon sequencing (16S and 18S rRNA) and PICRUSt2 were used to illustrate the microbial community structure and potential function in the optimal treatment at different developmental stages. Our results showed that exogenous microorganisms significantly promoted moss growth and increased aboveground biomass. After 30 days of cultivation, the Streptomyces pactum (1 g kg–1 substrate) + Chlorella vulgaris (3.33 L m–2) treatment presented optimal moss coverage, height, and density of 97.14%, 28.31 mm, and 2.28 g cm–2, respectively. The best-performing treatment had a higher relative abundance of Streptophyta—involved in moss growth—than the control. The control had significantly higher soil organic carbon than the best-performing treatment on day 30. Exogenous microorganisms improved eukaryotic community diversity and richness and may enhance soil microbial functional and metabolic diversity, such as growth and reproduction, carbon fixation, and cellulose and lignin decomposition, based on functional predictions. In summary, we identified the growth-promoting mechanisms of exogenous additives, providing a valuable reference for optimizing propagation technology for moss inoculum.

Effects of intercropping and nitrogen application on soil microbial metabolic functional diversity in maize cropping soil.

Soil microorganism is an important indicator of soil health and plays a critical role in biogeochemical processes. We collected soil samples from a multi-year in-situ field experiment with two cropping modes (maize monocropping and maize-potato intercropping) subjected to four nitrogen (N) levels (N0, 0 kg·hm-2; N125, 125 kg·hm-2; N250, 250 kg·hm-2; N375, 375 kg·hm-2). By using the Biolog-ECO microplate method, soil microbial metabolic activity, diversity and utilization of six carbon groups were analyzed. The results showed that N application significantly increased the average well color development (AWCD) values, Simpson and Shannon indices, with the highest value at N250 in mono- and inter-cropped soils. Moreover, N application promoted the utilization of amino acids, amines and phenolic compounds, but decreased the utilization of polymers. Compared with monocropping at the same N level, intercropping improved the AWCD values, Simpson and Shannon indices, with a maximal improvement at N250. Intercropping and nitrogen application significantly affected the metabolic activities of the six carbon-source groups. In addition, intercropping improved the utilization of labile carbon sources, such as amino acids and carbohydrates. Results of the redundancy analysis and linear regression showed that intercropping and N application elevated AWCD values by increasing soil temperature, water content, and soil organic carbon content. Therefore, the changes in soil physicochemical properties after intercropping were the main reason for the enhancement of microbial metabolic activity under N application.

Genome analysis of Pseudomonas sp. 14A reveals metabolic capabilities to support epiphytic behavior.

The surface of aboveground plant parts, known as the phyllosphere, is a habitat for various microorganisms called epiphytes establishing biotrophic interactions with their hosts. However, these communities can be affected by environmental and anthropogenic variations such as the application of agrochemicals. Thus, epiphytes have the capacity to survive in such environments. In this study, we obtained the genome of Pseudomonas sp. 14A, an epiphyte isolated from the pepper phyllosphere. The phylogenomic analyses suggested that Pseudomonas sp. 14A may be novel species closely related to P. moraviensis R28-S. Notably, the metabolic pathways proposed consistent with epiphytic lifestyle in Pseudomonas sp. 14A, were shared with other species displaying a different degree of phylogenetic relatedness. Furthermore, variations in configuration of metabolic gene clusters were observed, that could expand microbial metabolic diversity in close relatedness species, highlighting the relevance of microbial diversity associated with plants.

The metabolic diversity of soil microbial community in the petroleum exploitation area of Northern Shaanxi, China

In order to explore the changes of soil chemical properties and microbial metabolic diversity under different petroleum pollution levels, conventional soil detection technology and Biolog® technology were used to study the soil chemical properties and microbial community characteristics of the clean soil in the north Shaanxi oilfield under four different petroleum pollution gradients. The results showed that the soil after petroleum pollution had higher total organic carbon content, higher carbon nitrogen ratio and lower total nitrogen content. Petroleum had a significant effect on the metabolic capacity of soil microbial communities from carbon sources and their utilization patterns. There were significant differences in microbial community metabolism in petroleum-contaminated soils at different concentrations, with a decreasing trend with increasing contamination. At the same time, the microbial activity that could utilize carboxylic acid compounds and polymers was higher in the contaminated soil, while the microbial activity that utilized amino acids and carbohydrates was higher in the clean soil. With the increase of pollutant concentration, the metabolic pattern of soil microbial community to carbon sources changed from sugar-based to polymers-based. This indicates that oil pollution has changed the use of some preferred carbon sources by soil microorganisms, and long-term pollution will stabilize the carbon sources available to microorganisms and promote the development of microbial communities that prefer polymeric substances as carbon sources. This provides theoretical guidance and data support for the bioremediation and treatment of petroleum-contaminated soil in loess hilly areas.

Sugar profile regulates the microbial metabolic diversity in Chinese Baijiu fermentation

Cereals are widely used as raw material for food fermentation, and they can provide a variety of sugars in the fermentation via saccharification. However, the effect of sugar profile on microbial metabolism in spontaneous food fermentation is still unclear. Here, this work studied the regulation of sugar profile on the diversity of microbiota and their metabolism in Chinese Baijiu fermentation using sorghum as raw material. Six sugars were detected during Baijiu fermentation with 6 different cultivars of sorghum. The diversity of microbiota (ANOSIM: bacteria: P = 0.001, R = 0.77; fungi: P = 0.009, R = 0.33) and metabolites (ANOSIM: P = 0.001, R = 0.50) had different profiles during Baijiu fermentation. Among these sugars, glucose, fructose, and arabinose were identified as key sugars driving both the microbial and the metabolic diversity during Chinese Baijiu fermentation, and the metabolic diversity was positively correlated with the microbial diversity (P < 0.05). Hence, response surface methodology was used to establish a predictive model for regulating the metabolic diversity with the combination of three key sugars. The metabolic diversity significantly increased to 0.42 with the optimized levels of glucose (31.82 g/L), fructose (4.81 g/L), and arabinose (0.20 g/L), compared with unoptimized low-level average metabolic diversity (0.29). This work would provide a strategy to control microbial metabolism in spontaneous food fermentation, hence to improve the quality of fermented foods.