Microbial Functional Guilds Research Articles

Differential responses of soil bacteria, fungi and protists to root exudates and temperature

The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.

Effects of frequency and amount of stover mulching on the microbial community composition and structure in the endosphere and rhizosphere.

Stover mulching, as a sustainable agricultural conservation practice, has been shown to effectively increase soil organic matter and enhance crop yields. The impact of stover mulching on soil microorganisms has been extensively studied. However, less attention has been given to endophytic and rhizospheric microorganisms that have closer relationships with crops. How do the quality and frequency of stover mulching affect the composition and structure of these endosphere and rhizosphere microbial communities? And what is their influence on critical indicators of soil health such as bacterial plant pathogen and Rhizobiales? These questions remain unresolved. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching qualities (0%, 33%, 67%, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. Results showed significant correlations between Bacillales and Rhizobiales orders and soil SOC, NO3-N, and NH4+N; Hypocreales and Eurotiales orders were significantly correlated with soil NO3-N, with the Aspergillus genus also showing a significant correlation with soil SOC. The frequency and quality of stover mulching had a significant effect on root and rhizospheric microbial communities, with the lowest relative abundance of bacterial plant pathogens and highest relative abundance of nitrogen-fixing bacteria such as Rhizobiales and Hypocreales observed under F1/3 and F2/3 conditions. The most complex structures in endosphere and rhizospheric microbial communities were found under Q33 and Q67 conditions, respectively. This research indicates that from a soil health perspective, low-frequency high-coverage stover mulching is beneficial for the composition of endosphere and rhizosphere microbial communities, while moderate coverage levels are conducive to more complex structures within these communities. This study holds significant ecological implications for agricultural production and crop protection.

Dynamics of microbial functional guilds involved in the humification process during aerobic composting of chicken manure on an industrial scale.

Proper composting treatment of poultry manure waste is recommended before its use as a fertilizer. This involves many bioprocesses driven by microorganisms. Therefore, it is important to understand microbial mechanisms behind these bioprocesses in manure composting systems. Many efforts have been made to study the microbial community structure and diversity in these systems using high-throughput sequencing techniques. However, the dynamics of microbial interaction and functionality, especially for key microbial functional guilds, are not yet fully understood. To address these knowledge gaps, we collected samples from a 150-day industrial chicken manure composting system and performed the microbial network analysis based on the sequencing data. We found that the family Bacillaceae and genus Bacillus might play important roles in organic matter biodegradation at the mesophilic/thermophilic phases. Genera Virgibacillus, Gracilibacillus, Nocardiopsis, Novibacillus, and Bacillaceae_BM62 were identified as the key ones for humic acid synthesis at the mature phases. These findings improve our understanding about the fundamental mechanisms behind manure composting and can aid the development of microbial agents to promote manure composting performance.

Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments

Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.

Counteracting effects of soil biota on emergence and growth of herbaceous plants

BackgroundPlants condition the biotic composition of their rhizosphere. In turn, this plant legacy on the soil biota may affect the performance of plants recruiting in their vicinity. Unravelling how plant-soil legacies drive plant recruitment is key to understand vegetation dynamics and plant community assembly. Studies on the topic usually focus on the effects of soil microbiota as a whole, while the relative role of different guilds of soil organisms in the plant recruitment processes is not usually dissected.AimsHere, we used soils of Mediterranean woody plant species to test whether arbuscular mycorrhizal fungi (AMF) and small-size microbiota (< 50 µm) (MB) affect the germination success and growth of eight herbaceous plants.ResultsWe documented a significant increase in seedling emergence probability when small-sized MB was present and no effect of AMF. In contrast, the aboveground plant biomass decreased with the presence of MB and increased with that of AMF. Interestingly, those plants growing in the absence of MB and in soils from woody plants associated with higher AMF richness developed higher aboveground biomass.ConclusionThis study brings new evidence on how soil microbial communities can determine the performance of their associated herb community, and also, how the effects of different microbial guilds may change across the plant ontogeny. Given these results, the differential effect of soil microbial functional guilds should be considered to better understand plant soil legacies and feedbacks, potentially driving plant recruitment and community assembly.

Effects of common afforestation tree species on soil bacterial community and microbial functional guilds in subtropical forests.

To understand the effects of common afforestation tree species on soil microbial community in subtropical forests, seven different tree species were selected as the research object, including Pinus massoniana, Mytilaria laosensis, Liquidambar formosana, Ilex chinensis, Michelia macclurei, Quercus acutissima and Betula luminifera. Based on 16S rRNA high-throughput sequencing and real-time quantitative PCR techniques, we explored the effects of different tree species on soil bacterial community composition, diversity and microbial functional guilds. The results showed that Acidobacteria, Proteobacteria, and Actinobacteria were the dominant bacterial phyla, and that there was no significant difference in bacterial diversity or richness index among different tree species. Results of redundancy analysis suggested that soil bulk density, soil C/N, litter nitrogen content, and litter C/N were the predominant factors determining soil bacterial community composition. The afforestation tree species had significant effects on functional gene abundances of ammonia oxidizing archaea, ammonia oxidizing bacteria and complete ammonia oxidation. Comammox were dominant in abundance. Ammonia oxidizing archaea amoA gene was the only type whose abundance showed significant correlation with soil nitrate content, suggesting that ammonia oxidizing archaea could play a dominant role in the autotrophic nitrification in the acidic subtropical forest soils. The afforestation tree species had significant effects on functional gene abundances of ammonia oxidizing microorganisms. Results of correlation analysis showed that litter nitrogen content was the driving factor for the abundance of ammonia oxidizing microorganisms. Our study provided strong evidence that the responses of soil microbial functional guilds to tree species were more sensitive than bacterial community composition. Future studies should explore the mechanisms of tree plantations on forest ecosystem functioning from the perspective of microbial functional guilds.

Effects of frequency and amount of stover mulching on soil nitrogen and the microbial functional guilds of the endosphere and rhizosphere.

Stover mulching as a conservation and sustainable agricultural practice is beneficial for maintaining soil nitrogen (N) requirements and plant health. The microbial functional guilds of the root and rhizosphere are important factors in the soil nitrogen cycle. However, it is unclear how the frequency and amount of stover mulching influence microbial functional guilds in the root and rhizosphere. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching amounts (0, 1/3, 2/3, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. The bacterial functional guilds of nitrogen fixation, nitrification, and anaerobic nitrate oxidation displayed the significantly correlation with C/N, total nitrogen, NO3−, and NH4+. The fungal functional guilds of plant pathogens and saprotrophs showed significantly correlations with C/N, total nitrogen, and NO3−. Moreover, we found that bacterial guilds play a pivotal role in maintaining N requirements at the jointing stage, whereas root endophytic fungal guilds play a more important role than bacterial guilds in regulating plant health at the mature stage. The frequency and amount of stover mulching had significant effects on the microbial functional guilds in the root and rhizosphere. Our data suggest that stover mulch application twice every 3 years is the optimal mulching frequency because it yielded the lowest abundance of nitrifying and anaerobic nitrate-oxidising bacteria and the highest abundance of nitrogen-fixing bacteria at the jointing stage, as well as the lowest abundance of fungal plant pathogens in roots at the mature stage.

Ecological interactions among microbial functional guilds in the plant-soil system and implications for ecosystem function

Ecological interactions among microbial functional guilds in the plant-soil system and implications for ecosystem function

Century long fertilization reduces stochasticity controlling grassland microbial community succession

Determining the drivers underlying ecological succession is essential for predicting ecosystem functioning in response to human-induced environmental changes. Although various studies have examined the impacts of nitrogen (N) addition on plant and microbial community diversity, structure and activities, it remains unknown how long-term anthropogenic fertilization affects the ecological succession of microbial functional guilds and its underlying community assembly mechanisms. Here, using archived soils, we examined more than a century's succession in soil microbial functional communities (from 1870 to 2008) from the Park Grass Experiment at Rothamsted Experimental Station, the longest running ecological experiment in the world. Long-term fertilization was found to significantly alter soil functional community structure and led to increasingly convergent succession of soil microbial communities. The importance of stochastic assembly varied greatly in regulating the succession of different microbial guilds. Fertilization had large to medium effects on reducing ecological stochasticity for microbial guilds involved in carbon (C) fixation and degradation, nitrogen (N) fixation and mineralization, and denitrification. This century long-term study elucidated the differing influences of assembly mechanisms on soil microbial functional communities involved in C and N cycling, which has important implications for understanding and predicting the microbial mediated ecological consequences of human-induced environmental changes.

Sandy soils amended with bentonite induced changes in soil microbiota and fungistasis in maize fields

The addition of bentonite, used as soil conditioner, can promote sandy soil macro-aggregate formation, moisture content retention and increase soil nutrient concentrations. However, there is limited knowledge about how bentonite influences soil microbial communities and interconnections among community members associated with crops, such as maize in continuous production on sandy soils. Metabarcoding analysis of the fungal internal transcribed spacer 1 (ITS1) region and the bacterial 16S rRNA gene V4 region revealed that the fungal communities in sandy maize fields (dominated by Guehomyces, Alternaria and Mortierella) were more diverse and abundant in soils amended with bentonite than those without bentonite amendment. By contrast, the bacterial communities (dominated by Proteobacteria and Actinobacteria) had similar alpha-diversity under both conditions but many functional guilds, including those affiliated with fermentation and N-cycling, differed significantly in community compositional structure between soils with and without bentonite amendment. The increase in soil nutrient concentrations due to the addition of bentonite was a key factor associated with changes in the bacterial communities. However, the fungal communities were more strongly influenced by the capacity of bentonite to increase soil moisture retention and enhance macro-aggregate development. Molecular ecological network analysis revealed more competitive (62.1% of total significant associations) than cooperative (37.9%) associations among microbial community members across all soils studied. The observation that fungal phytopathogens recovered from bentonite-amended soils had more negative correlations (75.6%) with naturally occurring beneficial bacteria and/or fungi than those in non-bentonite soils (65.2%), perhaps suggests, although speculation, that the addition of bentonite promoted soil fungistasis. In summary, our study showed that the addition of bentonite increased maize productivity and reshaped the microbial functional guilds in sandy soils, a consequence of improved soil structure as well as water and nutrient retention; however, the amendment’s long-term impact on soil suppressiveness to fungal phytopathogens is worth further investigation.

The efficacy of 3,4-dimethylpyrazole phosphate on N2O emissions is linked to niche differentiation of ammonia oxidizing archaea and bacteria across four arable soils

The nitrification inhibitor, 3,4-dimethylpyrazole phosphate (DMPP), can be used to reduce N2O emissions from agricultural ecosystems. However, the effectiveness of DMPP varies among soils, and this is due to both abiotic (e.g. soil properties) and biotic factors (e.g. ammonia oxidizers and denitrifier communities). Understanding the nature of these effects is necessary to improve the efficacy of DMPP, therefore encouraging wider adoption and environmental benefits. In particular, soil microbial properties associated with variation in efficacy remain largely unknown. In this study four contrasting arable soils (a grey desert soil, an alluvial paddy soil, a loess-formed paddy soil, and a red soil), were characterized based on DMPP inhibition of N2O emissions and associated microbial functional guilds. DMPP significantly inhibited nitrification and N2O emissions, with an average inhibitory rate ranging from 41.7% in a red soil to 90.0% in a grey desert soil. Ammonia oxidizing bacteria (AOB) and archaea (AOA) exhibited contrasting response patterns to DMPP addition. Notably, suppression of N2O emissions by DMPP only occurred alongside fluctuations in AOB abundance. However, when AOB were inhibited, AOA abundance increased. Soil-dependent response patterns to DMPP were observed for ammonia oxidizers and denitrifiers in terms of community structure. Partial least squares path modeling (PLS-PM) found that abiotic factors, particularly pH, and biological factors such as ammonia oxidizer communities, were closely linked to N2O emissions. Our findings provide evidence that: (i) DMPP effectively inhibits nitrification through inhibiting the abundance of AOB across soil types; (ii) releasing AOA from the competition with AOB allows AOA to efficiently grow and multiply, even under high ammonium conditions; and (iii) abiotic factors play a more important role than biotic factors in soil N2O emissions.

Litter chemistry influences decomposition through activity of specific microbial functional guilds

AbstractNiche differentiation among species is a key mechanism by which biodiversity may be linked to ecosystem function. We tested a set of widely invoked hypotheses about the extent of niche differentiation in one of the most diverse communities on Earth, decomposer microorganisms, by measuring their response to changes in three abundant litter resources: lignin, cellulose, and nitrogen (N). To do this, we used the model system Arabidopsis thaliana to manipulate lignin, cellulose, and N availability and then used high‐throughput sequencing to measure the response of microbial communities during decay. Resequencing the decomposer communities after incubation of decomposed litter with pure substrates showed that groups of species had unique substrate use profiles, such that species organized into functional “guilds” of decomposers that were associated with individual litter chemicals. Low concentrations of lignin, cellulose, or N in the litter caused unique shifts in decomposer community composition after 1 yr of decay. Low cellulose plants had low levels of fungi in all decomposer guilds, low lignin plants had high levels of fungi in all decomposer guilds, and low N plants had low levels of fungi in decomposer guilds associated with sucrose and lignin. The relative abundance of decomposer guilds correlated with the total loss of individual litter chemicals during litter decay in the field. In addition, N fertilization shifted decomposer communities during both the early and later stages of decay to those dominated by decomposers in the cellulose guild. Our results contrast the assumption that major carbon (C) and N degradation mechanisms are uniform across whole decomposer communities and instead suggest that decomposition arises from complementarity among groups of metabolically distinct taxa.

Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching

Nitrogen leaching owing to elevated acid deposition remains the main ecosystem threat worldwide. We aimed to contribute to the understanding of the highly variable nitrate losses observed in Europe after acid deposition retreat. Our study proceeded in adjacent beech and spruce forests undergoing acidification recovery and differing in nitrate leaching. We reconstructed soil microbial functional characteristics connected with nitrogen and carbon cycling based on community composition. Our results showed that in the more acidic spruce soil with high carbon content, where Acidobacteria and Actinobacteria were abundant (Proteo:Acido = 1.3), the potential for nitrate reduction and loss via denitrification was high (denitrification: dissimilative nitrogen reduction to ammonium (DNRA) = 3). In the less acidic beech stand with low carbon content, but high nitrogen availability, Proteobacteria were more abundant (Proteo:Acido = 1.6). Proportionally less nitrate could be denitrified there (denitrification:DNRA = 1), possibly increasing its availability. Among 10 potential keystone species, microbes capable of DNRA were identified in the beech soil while instead denitrifiers dominated in the spruce soil. In spite of the former acid deposition impact, distinct microbial functional guilds developed under different vegetational dominance, resulting in different N immobilization potentials, possibly influencing the ecosystem’s nitrogen retention ability.

Phylogenetically distinct phylotypes modulate nitrification in a paddy soil.

Paddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using high-throughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaeal amoA gene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance of Nitrosospira-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), and Nitrospira-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of 13C-labeled DNA further revealed that 13CO2 was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA and Nitrobacter-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated with Nitrosospira sp. strain L115 and the Nitrosospira multiformis lineage and that the 13C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic "Candidatus Nitrososphaera gargensis," uncultured fosmid 29i4, and acidophilic "Candidatus Nitrosotalea devanaterra" lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields.

Microbiology of healing mud (fango) from Roman thermae aquae iasae archaeological site (Varaždinske Toplice, Croatia).

We found well-preserved, rocky artefacts that had been buried in the healing mud (fango) for more than 1,500 years at the Roman archaeological site at Varaždinske Toplice. This Roman pool with fango sediments and artefacts is fed from hot sulphidic springs. The fango exhibited nearly neutral pH, a high level of organic C, an elevated concentration of heavy metals and a high total microbial biomass, greater than 10(8) cells per gram of dry weight. The dominant microbes, assessed by molecular profiling (denaturing gradient gel electrophoresis), were affiliated with Thiobacillus, Sulfuricurvum, Polaromonas, and Bdellovibrio. Polymerase chain reaction screening for microbial functional guilds revealed the presence of sulphur oxidizers and methanogens but no sulphate reducers. The dominance of four Proteobacterial classes (α-, β-, δ- and ε-Proteobacteria) was confirmed by fluorescence in situ hybridisation; Actinobacteria were less abundant. Cultivable bacteria represented up to 23.4 % of the total bacterial counts when cultivation media was enriched with fango. These bacteria represented the genera Acinetobacter, Aeromonas, Arthrobacter, Comamonas, Ewingella, Flavobacterium, Pseudomonas, Rahnella and Staphylococcus. This study showed that the heterogeneous nature of fango at neutral pH created various microniches, which largely supported microbial life based on sulphur-driven, autotrophic denitrification.