Draft genome sequence of <i>Burkholderia sordidicola</i> S170, a potential plant growth promoter isolated from coniferous forest soil in the Czech Republic

Burkholderia species are key players in the accumulation of carbon from cellulose decomposition in coniferous forest ecosystems. We report here the draft genome of Burkholderia sordidicola strain S170, containing features associated with known genes involved in plant growth promotion, the biological control of plant diseases, and green remediation technologies

Editorial: Theme issue on the ecology of soil microorganisms

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Potential of cometabolic transformation of polysaccharides and lignin in lignocellulose by soil Actinobacteria

While it is known that several Actinobacteria produce enzymes that decompose polysaccharides or phenolic compounds in dead plant biomass, the occurrence of these traits in the environment remains largely unclear. The aim of this work was to screen isolated actinobacterial strains to explore their ability to produce extracellular enzymes that participate in the degradation of polysaccharides and their ability to cometabolically transform phenolic compounds of various complexities. Actinobacterial strains were isolated from meadow and forest soils and screened for their ability to grow on lignocellulose. The potential to transform 14C-labelled phenolic substrates (dehydrogenation polymer (DHP), lignin and catechol) and to produce a range of extracellular, hydrolytic enzymes was investigated in three strains of Streptomyces spp. that possessed high lignocellulose degrading activity. Isolated strains showed high variation in their ability to produce cellulose- and hemicellulose-degrading enzymes and were able to mineralise up to 1.1% and to solubilise up to 4% of poplar lignin and to mineralise up to 11.4% and to solubilise up to 64% of catechol, while only minimal mineralisation of DHP was observed. The results confirm the potential importance of Actinobacteria in lignocellulose degradation, although it is likely that the decomposition of biopolymers is limited to strains that represent only a minor portion of the entire community, while the range of simple, carbon-containing compounds that serve as sources for actinobacterial growth is relatively wide.Peer reviewe

Temporal turnover of the soil microbiome composition is guild-specific

Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.Peer reviewe

Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood

Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.Peer reviewe

Moss biocrust accelerates the recovery and resilience of soil microbial communities in fire-affected semi-arid Mediterranean soils

After wildfires inMediterraneanecosystems,ruderalmossesarepioneerspecies,stabilizing the soilsurface previous to the establishment of vascular vegetation. However, little is known about the implication of pioneer moss biocrusts for the recovery and resilience of soils in early post-fire stages in semi-arid areas. Therefore, we studied the effects of the burgeoning biocrust on soil physicochemical and biochemical properties and the diversity and composition of microbial communities after a moderate-to-high wildfire severity. Seven months afterthe wildfire, the biocrust softened the strong impact ofthefireinsoils, affecting thediversity and composition ofbacteriaand fungicommunitycompared to the uncrusted soils exposed to unfavourable environmental stress. Soil moisture, phosphorous, and enzyme activities representing the altered biogeochemical cycles after the fire, were the main explanatory variables for biocrust microbial community compositionunderthesemi-arid conditions. High bacterial diversity was found in soils under mosses, while long-lasting legacies are expected in the fungal community, which showed greater sensitivity to the fire. The compositionof bacterial andfungal communities atseveral taxonomical levelswas profoundly alteredbythepresence of the moss biocrust, showing a rapid successional transition toward the unburned soil community. Pioneer moss biocrust play an important role improving the resilience of soil microbial communities. In the context of increasing f ire intensity, studying the moss biocrust effects on the recovery of soils microbiome is essential to understanding the resistance and resilience of Mediterranean forests to wildfire

Tree species identity alters decomposition of understory litter and associated microbial communities : a case study

Investigations on how tree species modify decomposition of understory litter have rarely been conducted, although potentially having impacts on soil carbon stocks and stability. The aim of our study was to disentangle the effects different tree species (alder, spruce, oak, and willow) exert on litter decomposition by comparing decomposition patterns and microbial measures (phospholipid fatty acids and microbial DNA) of both tree and understory (Calamagrostis epigejos) litter exposed at the respective tree species stands of a common garden experiment. An initially uniform mass loss of understory litter exposed at the stands suggests that inherent litter quality (assessed by C:N ratios and lignin content) was the major driver in early decomposition. However, in later stages of our experiment, decomposition of understory litter began to differ among the stands, suggesting a delayed tree species effect. Here, differences in microbial community composition caused by tree species identity (e.g., through varying N supply or phenolics leached from low-quality litter) were likely the major determinants affecting the decomposition of understory litter. However, in these advanced decomposition stages, tree species identity only partly altered microbial communities associated with understory litter. These results indicate that the development of microbial communities on understory litter (and its decay) is likely a combined result of inherent chemical composition and tree species identity.Peer reviewe