Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in decaying wood

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

BACKGROUND

Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.

RESULTS

Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.

CONCLUSIONS

This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.

Functionality of bacterial communities in constructed wetlands used for water purification: influence of root components and seasonality

Introduction

Constructed wetlands have become crucial ecosystems for the purification of industrial and agricultural water. The health of wetland plants and the efficacy of water purification are strongly influenced by root-associated bacteria. However, our understanding of the functions of bacterial communities in the plant different root components (i.e., rhizosphere, rhizoplane, and endosphere) and their impact on water purification is still limited.

Methods

To address this knowledge gap, we employed high-resolution 16S rRNA deep amplicon sequencing to explore the bacterial community structure and assembly within the root components of three plant species (i.e. Iris ensata, Canna indica, and Hymenocallis littoralis) found in constructed wetlands.

Results

Our findings revealed that the pollutant removal efficiency was higher in the wet season than in the dry season. The specific root compartment, plant species, environmental factors, and seasonality significantly influenced the bacterial composition, diversity and abundance. Across all three plant species, Proteobacteria emerged as the dominant bacterial groups in all root components. The abundance and diversity of bacterial communities exhibited a decline from the rhizosphere to the endosphere, accompanied by an increase in the number of distinctive biomarkers from the rhizosphere to the endosphere. The bacterial composition exhibited significant similarity in the rhizosphere in the dry season and the endosphere in the wet season. Bacterial genes in the rhizosphere-rhizoplane were associated with environmental information processing, transportation and metabolism, while those in the rhizoplane-endosphere primarily handle metabolic processes. The bacterial community positively correlated with total nitrogen content, chemical oxygen demand, and NO4 +-N in the dry season, while associated with total phosphorus, total organic carbon, and NO3 +-N content in the wet season.

Discussion

The structure and function of the bacterial community within the root rhizoplane-endosphere can serve as indicators of the water purification efficacy of constructed wetlands.

Two Paenibacillus spp. strains promote grapevine wood degradation by the fungus Fomitiporia mediterranea: from degradation experiments to genome analyses

Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc.

Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans

The basidiomycete Serpula lacrymans is responsible for major timber devastation in houses. Basidiomycetes are known to harbour a diverse but poorly understood microbial community of bacteria, archaea, yeasts and filamentous fungi. In this study, we used amplicon-sequencing to analyse the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the 'background' community structure. Our findings indicate that bacterial genera cluster depended on sample type and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground samples. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and lifestyle.

The Necrobiome of Deadwood: The Life after Death

In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and habitats for a wide variety of saprotrophic and heterotrophic organisms and significantly contributes to soil formation and carbon storage. Deadwood is inhabited by a plethora of organisms from various kingdoms that have evolved the ability to utilize decaying organic matter. This community, consisting of both eukaryotic and prokaryotic species, can be defined as “necrobiome”. Through the interactions between its various members, the necrobiome influences the decay rates of deadwood and plays a crucial role in the balance between organic matter decomposition, carbon sequestration, and gas exchanges (e.g., CO2) with the atmosphere. The present work aims to provide an overview of the biodiversity and role of the microbial communities that inhabit deadwood and their possible involvement in greenhouse gas (CO2, N2O, and CH4) emissions.

Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate

Two novel strains, HW T2.11^T and HW T5.17^T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11^T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17^T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C_19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11^T and HW T5.17^T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11^T (DSM 111006^T; UBOCC-M-3364^T) and HW T5.17^T (DSM 111007^T; UBOCC-M-3365^T).

Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood

Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass.

Measurement(s)	metagenomic data • metatranscriptomic data • microbiome • RNA-seq of total RNA
Technology Type(s)	DNA sequencing • RNA-seq of total RNA • amplicon sequencing • RNA sequencing
Factor Type(s)	time of decomposition
Sample Characteristic - Organism	Fungi • Bacteria
Sample Characteristic - Environment	wood
Sample Characteristic - Location	Narodni prirodni rezervace Zofinsky prales

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14821752

Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components

Fungi are considered to cause grapevine trunk diseases such as esca that result in wood degradation. For instance, the basidiomycete Fomitiporia mediterranea (Fmed) is overabundant in white rot, a key type of wood‐necrosis associated with esca. However, many bacteria colonize the grapevine wood too, including the white rot. In this study, we hypothesized that bacteria colonizing grapevine wood interact, possibly synergistically, with Fmed and enhance the fungal ability to degrade wood. We isolated 237 bacterial strains from esca‐affected grapevine wood. Most of them belonged to the families Xanthomonadaceae and Pseudomonadaceae. Some bacterial strains that degrade grapevine‐wood components such as cellulose and hemicellulose did not inhibit Fmed growth in vitro. We proved that the fungal ability to degrade wood can be strongly influenced by bacteria inhabiting the wood. This was shown with a cellulolytic and xylanolytic strain of the Paenibacillus genus, which displays synergistic interaction with Fmed by enhancing the degradation of wood structures. Genome analysis of this Paenibacillus strain revealed several gene clusters such as those involved in the expression of carbohydrate‐active enzymes, xylose utilization and vitamin metabolism. In addition, certain other genetic characteristics of the strain allow it to thrive as an endophyte in grapevine and influence the wood degradation by Fmed. This suggests that there might exist a synergistic interaction between the fungus Fmed and the bacterial strain mentioned above, enhancing grapevine wood degradation. Further step would be to point out its occurrence in mature grapevines to promote esca disease development.

Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition

Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N₂ fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N₂ fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.

Coarse woody debris decomposition assessment tool: Model development and sensitivity analysis

Coarse woody debris (CWD) is an important component in forests, hosting a variety of organisms that have critical roles in nutrient cycling and carbon (C) storage. We developed a process-based model using literature, field observations, and expert knowledge to assess woody debris decomposition in forests and the movement of wood C into the soil and atmosphere. The sensitivity analysis was conducted against the primary ecological drivers (wood properties and ambient conditions) used as model inputs. The analysis used eighty-nine climate datasets from North America, from tropical (14.2° N) to boreal (65.0° N) zones, with large ranges in annual mean temperature (26.5°C in tropical to -11.8°C in boreal), annual precipitation (6,143 to 181 mm), annual snowfall (0 to 612 kg m^-2), and altitude (3 to 2,824 m above mean see level). The sensitivity analysis showed that CWD decomposition was strongly affected by climate, geographical location and altitude, which together regulate the activity of both microbial and invertebrate wood-decomposers. CWD decomposition rate increased with increments in temperature and precipitation, but decreased with increases in latitude and altitude. CWD decomposition was also sensitive to wood size, density, position (standing vs downed), and tree species. The sensitivity analysis showed that fungi are the most important decomposers of woody debris, accounting for over 50% mass loss in nearly all climatic zones in North America. The model includes invertebrate decomposers, focusing mostly on termites, which can have an important role in CWD decomposition in tropical and some subtropical regions. The role of termites in woody debris decomposition varied widely, between 0 and 40%, from temperate areas to tropical regions. Woody debris decomposition rates simulated for eighty-nine locations in North America were within the published range of woody debris decomposition rates for regions in northern hemisphere from 1.6° N to 68.3° N and in Australia.

Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans

The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.

Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition

In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.

Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil

Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3-13 µmols C g-1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g-1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.

The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota)

Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Acidobacteriota strains growth and microbial isolation.

Function of sesquiterpenes from Schizophyllum commune in interspecific interactions

Wood is a habitat for a variety of organisms, including saprophytic fungi and bacteria, playing an important role in wood decomposition. Wood inhabiting fungi release a diversity of volatiles used as signaling compounds to attract or repel other organisms. Here, we show that volatiles of Schizophyllum commune are active against wood-decay fungi and bacteria found in its mycosphere. We identified sesquiterpenes as the biologically active compounds, that inhibit fungal growth and modify bacterial motility. The low number of cultivable wood inhabiting bacteria prompted us to analyze the microbial community in the mycosphere of S. commune using a culture-independent approach. Most bacteria belong to Actinobacteria and Proteobacteria, including Pseudomonadaceae, Sphingomonadaceae, Erwiniaceae, Yersiniaceae and Mariprofundacea as the dominating families. In the fungal community, the phyla of ascomycetes and basidiomycetes were well represented. We propose that fungal volatiles might have an important function in the wood mycosphere and could meditate interactions between microorganisms across domains and within the fungal kingdom.

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition

Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers.

Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO₂ emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO₂ efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.

IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.

Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood

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.

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.

Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids

Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.

Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia"

Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however, the impact of these metals on their growth and metabolism is not known. In order to gain insight into this relationship, we evaluated the effect of trace element solution SL10 on the growth of two strains (5B5 and WH15) of Acidobacteria belonging to the genus Granulicella and studied the proteomic responses to manganese (Mn). Granulicella species had highest growth with the addition of Mn, as well as higher tolerance to this metal compared to seven other metal salts. Variations in tolerance to metal salt concentrations suggests that Granulicella sp. strains possess different mechanisms to deal with metal ion homeostasis and stress. Furthermore, Granulicella sp. 5B5 might be more adapted to survive in an environment with higher concentration of several metal ions when compared to Granulicella sp. WH15. The proteomic profiles of both strains indicated that Mn was more important in enhancing enzymatic activity than to protein expression regulation. In the genomic analyses, we did not find the most common transcriptional regulation of Mn homeostasis, but we found candidate transporters that could be potentially involved in Mn homeostasis for Granulicella species. The presence of such transporters might be involved in tolerance to higher Mn concentrations, improving the adaptability of bacteria to metal enriched environments, such as the decaying wood-rich Mn environment from which these two Granulicella strains were isolated.

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

RP11^T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11^T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr^-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731^T, Paraburkholderia fungorum LMG 16225^T and Paraburkholderia caffeinilytica CF1^T. Strain RP11^T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11^T from its closest relatives, including growth on phthalic acid. Strain RP11^T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11^T was Q-8, and the major cellular fatty acids were C_16 : 0, 3OH-C_16 : 0, C_17 : 0 cyclo, C_19 : 0 cyclo ω8c, and summed feature 8 (C_18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11^T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11^T (=DSM 110123^T=LMG 31517^T).

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.

Biodegradability of woody film produced by solvent volatilisation of Japanese Beech solution

To address the problem of marine pollution from discarded plastics, we developed a highly biodegradable woody film, with almost the same components as wood, from the formic acid solution of ball-milled wood. We found that the woody film was not easily degraded by cultured solution of hand bacteria (phylum Proteobacteria was dominant). However, the film was easily biodegraded when in cultured solution of soil (Firmicutes, especially class Bacilli, was dominant) for 4 weeks at 37 °C, or when buried in the soil itself, both under aerobic conditions (Acidobacteria and Proteobacteria were dominant) for 40 days at room temperature and under anaerobic conditions (Firmicutes, especially family Ruminococcaceae, was dominant) for 5 weeks at 37 °C. Moreover, when film was buried in the soil, more carbon dioxide was generated than from soil alone. Therefore, the film was not only brittle but formed of decomposable organic matter. We showed that the film does not decompose at the time of use when touched by the hand, but it decomposes easily when buried in the soil after use. We suggest that this biodegradable woody film can be used as a sustainable raw material in the future.

Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes

Wood decomposition, a critical process in carbon and nutrient cycles, is influenced by environmental conditions, decomposer communities and substrate composition. While these factors differ between land and stream habitats, across-habitat comparisons of wood decay processes are rare, limiting our ability to evaluate the context- dependency of the drivers of decay. Here we tracked wood decomposition of three tree species placed in stream and terrestrial habitats in a lowland tropical forest in Panama. At 3 and 11 months we measured mass loss, wood nitrogen and wood polymer concentrations, and sampled wood-associated fungal and bacterial communities. After 11 months of decay we found that mass loss occurred 9% faster in streams than on land, but loss of cellulose, hemicellulose and lignin did not differ between habitats. We also observed large differences in microbial decomposer communities between habitats. Overall, we found faster mass loss of wood in water, but no differences in biotic decay processes between habitats despite distinct microbial communities in streams and on land. Our research challenges the assumption that wood decays relatively slowly in water reflecting unfavorable environmental conditions and a limited capacity of aquatic microbial communities to effectively degrade wood polymers.

Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae)

The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.

Microbial succession on decomposing root litter in a drought-prone Scots pine forest

Decomposition is a major flux of the carbon cycle in forest soils and understanding the involved processes is a key for budgeting carbon turnover. Decomposition is constrained by the presence of biological agents such as microorganisms and the underlying environmental conditions such as water availability. A metabarcoding approach of ribosomal markers was chosen to study the succession of bacterial and fungal decomposers on root litter. Litterbags containing pine roots were buried in a pine forest for two years and sequentially sampled. Decomposition and the associated communities were surveyed under ambient dry and long-term irrigation conditions. Early decomposition stages were characterized by the presence of fast-cycling microorganisms such as Bacteroidetes and Helotiales, which were then replaced by more specialized bacteria and litter-associated or parasitic groups such as Acidobacteria, white rots, and Pleosporales. This succession was likely driven by a decrease of easily degradable carbohydrates and a relative increase in persistent compounds such as lignin. We hypothesize that functional redundancy among the resident microbial taxa caused similar root decomposition rates in control and irrigated forest soils. These findings have important implications for drought-prone Alpine forests as frequent drought events reduce litter fall, but not litter decomposition, potentially resulting in lower carbon stocks.

Microbial Diversity in Decaying Oil Palm Empty Fruit Bunches (OPEFB) and Isolation of Lignin-degrading Bacteria from a Tropical Environment

Oil palm empty fruit bunches (OPEFB) are the most abundant, inexpensive, and environmentally friendly lignocellulosic biomass in Malaysia. Investigations on the microbial diversity of decaying OPEFB may reveal microbes with complex enzymes that have the potential to enhance the conversion of lignocellulose into second-generation biofuels as well as the production of other value-added products. In the present study, fungal and bacterial diversities in decaying OPEFB were identified using Illumina MiSeq sequencing of the V3 region of the 16S rRNA gene and V4 region of the 18S rRNA gene. Fungal diversity in decaying OPEFB was dominated by the phylum Ascomycota (14.43%), while most of the bacterial sequences retrieved belonged to Proteobacteria (76.71%). Three bacterial strains isolated from decaying OPEFB, designated as S18, S20, and S36, appeared to grow with extracted OPEFB-lignin and Kraft lignin (KL) as the sole carbon source. 16S rRNA gene sequencing identified the 3 isolates as Paenibacillus sp.. The molecular weight distribution of KL before and after degradation showed significant depolymerization when treated with bacterial strains S18, S20, and S36. The presence of low-molecular-weight lignin-related compounds, such as vanillin and 2-methoxyphenol derivatives, which were detected by a GC-MS analysis, confirmed the KL-degrading activities of isolated Paenibacillus strains.

Effect of Organic Carbon and Nitrogen on the Interactions of Morchella spp. and Bacteria Dispersing on Their Mycelium

In this study we investigated how the source of organic carbon (Corg) and nitrogen (Norg) affects the interactions between fungi of the genus Morchella and bacteria dispersing along their hyphae (fungal highways; FH). We demonstrated that bacteria using FH increase the hydrolysis of an organic nitrogen source that only the fungus can degrade. Using purified fungal exudates, we found that this increased hydrolysis was due to bacteria enhancing the activity of proteolytic enzymes produced by the fungus. The same effect was shown for various fungal and bacterial strains. The effect of this enhanced proteolytic activity on bacterial and fungal biomass production varied accordingly to the source of Corg and Norg provided. An increase in biomass for both partners 5 days post-inoculation was only attained with a Norg source that the bacterium could not degrade and when additional Corg was present in the medium. In contrast, all other combinations yielded a decrease on biomass production in the co-cultures compared to individual growth. The coupled cycling of Corg and Norg is rarely considered when investigating the role of microbial activity on soil functioning. Our results show that cycling of these two elements can be related through cross-chemical reactions in independent, albeit interacting microbes. In this way, the composition of organic material could greatly alter nutrient turnover due to its effect on the outcome of interactions between fungi and bacteria that disperse on their mycelia.

Molecular fungal community and its decomposition activity in sapwood and heartwood of 13 temperate European tree species

Deadwood is an important structural component in forest ecosystems and plays a significant role in global carbon and nutrient cycling. Relatively little is known about the formation and decomposition of CWD by microbial communities in situ and about the factors controlling the associated processes. In this study, we intensively analyzed the molecular fungal community composition and species richness in relation to extracellular enzyme activity and differences in decomposing sapwood and heartwood of 13 temperate tree species (four coniferous and nine deciduous species, log diameter 30–40 cm and 4 m long) in an artificial experiment involving placing the logs on the forest soil for six years. We observed strong differences in the molecular fungal community composition and richness among the 13 tree species, and specifically between deciduous and coniferous wood, but unexpectedly no difference was found between sapwood and heartwood. Fungal species richness correlated positively with wood extractives and negatively with fungal biomass. A distinct fungal community secreting lignocellulolytic key enzymes seemed to dominate the decomposition of the logs in this specific phase. In particular, the relative sequence abundance of basidiomycetous species of the Meruliaceae (e.g. Bjerkandera adusta) correlated with ligninolytic manganese peroxidase activity. Moreover, this study reveals abundant white-rot causing Basidiomycota and soft-rot causing Ascomycota during this phase of wood decomposition.

Allelopathy of Wild Mushrooms—An Important Factor for Assessing Forest Ecosystems in Japan

Research Highlights: Some organisms such as plants and fungi release certain secondary metabolites, generally called allelochemicals, which can influence the organisms around them. Some of the secondary metabolites released by mushrooms may have certain effects on the growth and development of neighboring plants. Background Objectives: The purpose of the present study was to investigate the allelopathic potential of mushrooms in a forest ecosystem. To this end, 289 Japanese mushroom species were collected from the wild and tested using a modified sandwich method, which is a quick and effective bioassay technique. Materials and Methods: The collected specimens were prepared for bioassay as dried samples, and 10 mg/well (10 cm2) was added to a 6-well multidish according to the mycelia biomass, which was estimated at 700−900 kg ha−1 year−1 (7–9 mg 10 cm−2) in coniferous forests. Results: Of the screened mushroom species, 74% inhibited more than 50% of the radicle elongation in lettuce (Lactuca sativa var. Great Lakes 366) seedlings, while the average of all species was 41.1%. This result suggests that wild mushrooms have a significant regulatory effect on lettuce growth. According to our standard deviation variance analysis, 54 out of 289 species showed significant allelopathic activity. Among these species, Xeromphalina tenuipes, Cortinarius violaceus, and Clavaria miyabeana exhibited the strongest growth inhibitory activity, with radicle elongation of 5.1%, 4.3%, and 7.6% of the control, respectively. In contrast, Ischnoderma resinosum stimulated the length of radicle and hypocotyl growth by 30.6% and 42.0%, respectively. These results suggest that these species may play important roles in ecosystems. In addition, the wide range of allelopathic activities observed in mushrooms indicates that various amounts of diverse secondary metabolites from these species are involved in mushroom allelopathy. Conclusions: Our study reveals the importance of evaluating mushroom allelopathy to understand the wider ecological structures within complex ecosystems.

Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes

Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.

Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of ¹³C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated ¹³C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.

Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph

For the past 60 years Caulobacter spp. have been commonly attributed an aquatic and oligotrophic lifestyle yet are not uncommon in nutrient-rich or soil environments. This study evaluates the environmental and ecological associations of Caulobacter to reconcile past evidence, largely limited to culturing and microscopy, with currently available metagenomic and genomic data. The distribution of Caulobacter species and their characteristic adhesion-conferring genes, holdfast (hfaAB), were determined using collections of 10,641 16S rRNA gene libraries (196 studies) and 2625 shotgun metagenomes (190 studies) from a range of terrestrial and aquatic environments. Evidence for ecotypic variation was tested in 26 genomes sourced from soil, rhizosphere, plant, groundwater, and water. Caulobacter were, on average, fourfold more relatively abundant in soil than in aquatic environments, and abundant in decomposing wood, compost, and particulate matter (in air and water). Caulobacter holdfast genes were 35-fold more abundant in soils than aquatic environments. Ecotypic differences between soil and aquatic Caulobacter were evident in the environmental associations of several species and differences in genome size and content among isolates. However, most abundant species were common to both environments, suggesting populations exist in a continuum that was evident in the re-analysis of studies on the temporal dynamics of, and sources of bacterioplankton to, lakes and rivers. This study provides a new perspective on the ecological profile of Caulobacter, demonstrating that members of this genus are predominantly soil-borne, possess an overlooked role in plant matter decomposition and a dependency on water-mediated dispersal.

Bacteria associated with decomposing dead wood in a natural temperate forest

Dead wood represents an important pool of organic matter in forests and is one of the sources of soil formation. It has been shown to harbour diverse communities of bacteria, but their roles in this habitat are still poorly understood. Here, we describe the bacterial communities in the dead wood of Abies alba, Picea abies and Fagus sylvatica in a temperate natural forest in Central Europe. An analysis of environmental factors showed that decomposing time along with pH and water content was the strongest drivers of community composition. Bacterial biomass positively correlated with N content and increased with decomposition along with the concurrent decrease in the fungal/bacterial biomass ratio. Rhizobiales and Acidobacteriales were abundant bacterial orders throughout the whole decay process, but many bacterial taxa were specific either for young (<15 years) or old dead wood. During early decomposition, bacterial genera able to fix N2 and to use simple C1 compounds (e.g. Yersinia and Methylomonas) were frequent, while wood in advanced decay was rich in taxa typical of forest soils (e.g. Bradyrhizobium and Rhodoplanes). Although the bacterial contribution to dead wood turnover remains unclear, the community composition appears to reflect the changing conditions of the substrate and suggests broad metabolic capacities of its members.

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.

Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications

Acidobacteria have been described as one of the most abundant and ubiquitous bacterial phyla in soil. However, factors contributing to this ecological success are not well elucidated mainly due to difficulties in bacterial isolation. Acidobacteria may be able to survive for long periods in soil due to protection provided by secreted extracellular polymeric substances that include exopolysaccharides (EPSs). Here we present the first study to characterize EPSs derived from two strains of Acidobacteria from subdivision 1 belonging to Granulicella sp. EPS are unique heteropolysaccharides containing mannose, glucose, galactose and xylose as major components, and are modified with carboxyl and methoxyl functional groups that we characterized by Fourier transform infrared (FTIR) spectroscopy. Both EPS compounds we identified can efficiently emulsify various oils (sunflower seed, diesel, and liquid paraffin) and hydrocarbons (toluene and hexane). Moreover, the emulsions are more thermostable over time than those of commercialized xanthan. Acidobacterial EPS can now be explored as a source of biopolymers that may be attractive and valuable for industrial applications due to their natural origin, sustainability, biodegradability and low toxicity.

Bacteria in decomposing wood and their interactions with wood-decay fungi

The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.

Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria

Acidobacteria is one of the most abundant phyla in soils and has been detected in rhizosphere mainly based on cultivation-independent approaches such as 16S rRNA gene survey. Although putative interaction of Acidobacteria with plants was suggested, so far no plant–bacterial interactions were shown. Therefore, we performed several in vitro tests to evaluate Acidobacteria–plant interactions and the possible mechanisms involved in such interaction. We observed that Arabidopsis thaliana inoculated with three strains belonging to Acidobacteria subdivision 1 showed increase in biomass of roots and shoots as well as morphological changes in root system. Our results indicate that the plant hormone indole-3-acetic acid production and iron acquisition are plausibly involved in the plant and Acidobacteria interactions. Here, we confirm for the first time that Acidobacteria can actively interact with plants and act as plant growth-promoting bacteria. In addition, we show that Acidobacteria strains produce exopolysaccharide which supports the adhesion of bacteria to the root surfaces.

Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs

Prokaryotes colonize decaying wood and contribute to the degradation process, but the dynamics of prokaryotic communities during wood decay is still poorly understood. We studied the abundance and community composition of Bacteria and Archaea inhabiting naturally decaying Picea abies logs and tested the hypothesis that the variations in archaeal and bacterial abundances and community composition are coupled with environmental parameters related to the decay process. The data set comprises >500 logs at different decay stages from five geographical locations in south and central Finland. The results show that Bacteria and Archaea are an integral and dynamic component of decaying wood biota. The abundances of bacterial and archaeal 16S rRNA genes increase as wood decay progresses. Changes in bacterial community composition are clearly linked to the loss of density of wood, while specific fungal-bacterial interactions may also affect the distribution of bacterial taxa in decaying wood. Thaumarchaeota were prominent members of the archaeal populations colonizing decaying wood, providing further evidence of the versatility and cosmopolitan nature of this phylum in the environment. The composition and dynamics of the prokaryotic community suggest that they are an active component of biota that are involved in processing substrates in decaying wood material.

Bacterial Community Succession in Pine-Wood Decomposition

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood

Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.

A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies

Deadwood is an important biodiversity hotspot in forest ecosystems. While saproxylic insects and wood-inhabiting fungi have been studied extensively, little is known about deadwood-inhabiting bacteria. The study we present is among the first to compare bacterial diversity and community structure of deadwood under field conditions. We therefore compared deadwood logs of two temperate forest tree species Fagus sylvatica and Picea abies using 16S rDNA pyrosequencing to identify changes in bacterial diversity and community structure at different stages of decay in forest plots under different management regimes. Alphaproteobacteria, Acidobacteria and Actinobacteria were the dominant taxonomic groups in both tree species. There were no differences in bacterial OTU richness between deadwood of Fagus sylvatica and Picea abies. Bacteria from the order Rhizobiales became more abundant during the intermediate and advanced stages of decay, accounting for up to 25% of the entire bacterial community in such logs. The most dominant OTU was taxonomically assigned to the genus Methylovirgula, which was recently described in a woodblock experiment of Fagus sylvatica. Besides tree species we were able to demonstrate that deadwood physico-chemical properties, in particular remaining mass, relative wood moisture, pH, and C/N ratio serve as drivers of community composition of deadwood-inhabiting bacteria.