Coniferous Forest Soils Research Articles

Rhizosphere activity and atmospheric methane concentrations drive variations of methane fluxes in a temperate forest soil

Aerated soils represent an important sink for atmospheric methane (CH4), due to the effect of methanotrophic bacteria, thus mitigating current atmospheric CH4 increases. Whilst rates of CH4 oxidation have been linked to types of vegetation cover, there has been no systematic investigation of the interaction between plants and soil in relation to the strength of the soil CH4 sink. We used quasi-continuous automated chamber measurements of soil CH4 and CO2 flux from soil collar treatments that selectively include root and ectomycorrhizal (ECM) mycelium to investigate the role of rhizosphere activity as well as the effects of other environmental drivers on CH4 uptake in a temperate coniferous forest soil. We also assessed the potential impact of measurement bias from sporadic chamber measurements in altering estimates of soil CO2 efflux and CH4 uptake. Results show a clear effect of the presence of live roots and ECM mycelium on soil CO2 efflux and CH4 uptake. The presence of ECM hyphae alone (without plant roots) showed intermediate fluxes of both CO2 and CH4 relative to soils that either contained roots and ECM mycelium, or soil lacking root- and ECM mycelium. Regression analysis confirmed a significant influence of soil moisture as well as temperature on flux dynamics of both CH4 and CO2 flux. We further found a surprising increase in soil CH4 uptake during the night, and discuss diurnal fluctuations in atmospheric CH4 (with higher concentrations during stable atmospheric conditions at night) as a potential driver of CH4 oxidation rates. Using the high temporal resolution of our data set, we show that low-frequency sampling results in systematic bias of up-scaled flux estimates, resulting in under-estimates of up to 20% at our study site, due to fluctuations in flux dynamics on diurnal as well as longer time scales.

14C mean residence time and its relationship with thermal stability and molecular composition of soil organic matter: A case study of deciduous and coniferous forest types

Soil organic matter (SOM) plays a critical role in the global terrestrial carbon cycle, and a better understanding of soil processes involved in SOM stability is essential to determine how projected climate-driven changes in soil processes will influence carbon dynamics. We used 14C signature, analytical thermal analysis, and ultrahigh resolution mass spectrometry to determine the influence of deciduous and coniferous forest vegetation type and soil depth on the stability of soil C. The 14C mean residence time (MRT) of the illuvial B horizon soils averaged 1350years for the deciduous soils and 795years for the coniferous soils. The difference of MRT between mineral soils by forest type may be due to the saturation of extractable Fe and Al minerals binding sites by SOM in the coniferous soils, allowing greater transport of modern SOM from the O horizon down the soil profile, as compared with the non-saturated minerals in the deciduous soil profile. The molecular mass distribution of the deciduous water-extractable aromatic SOM fraction was shifted to a lower mass range in the lower portion of B horizon soil compared with the upper portion, indicating preferential sorption of the higher mass aromatic fraction. The shift in the mass distribution of the aromatic fraction in the coniferous soil was much less than in the deciduous soil, which supports the view that the extractable metal minerals had reached saturation. We conclude that greater transport of modern O horizon SOM to the lower mineral B horizons in the coniferous soil profile resulted in its radiocarbon enrichment and shorter estimated MRT. Our findings highlight the importance of forest vegetation type, soil depth and transport mechanisms on SOM stability, and suggest important ecological implications for changes in forest composition on the terrestrial C cycle.

Evaluation of the mixing of sands into soils on nitrification potential from different land-use systems

Quartz sand is often mixed with soil to enable leaching in studies where nitrate leaching is simulated. However, the addition of sand may also have an effect on the N transformations dynamics but this aspect has never been studied so far. A15N tracer experiment was conducted to investigate this effect on coniferous forest soil (CF), rice-rice rotation soil (RR), rice-wheat rotation soil (RW) and maize-wheat rotation soil (MW). Results showed that the addition of quartz sand into the three agricultural soils (RR, RW and MW) reduced the net production of NO3−-N, but the mechanisms involved in the reduction among the three soils were different. In the RR soil, the addition of quartz sand had no effect on gross NO3−-N production (autotrophic nitrification + heterotrophic nitrification), but enhanced gross NO3−-N consumption (NO3−-N immobilization + dissimilatory NO3− reduction to NH4+), resulting in reduced NO3−-N built-up. In the RW soil, the addition of quartz sand significantly inhibited gross autotrophic nitrification rates and stimulated gross NO3−-N immobilization rate. In the MW soil, only dissimilatory NO3− reduction to NH4+ (DNRA) rate was stimulated by the addition of quartz sand. In contrast, in the CF soil sand addition did not have an effect on the gross N transformation rates. Our results show that sand additions will alter N transformations dynamics in an unforeseeable manner and should be considered with the utmost caution.

Characteristics of Fungi Community Structure and Genetic Diversity of Forests in Guandi Mountains

Soil microorganisms drive the biogeochemical process of carbon, nitrogen, phosphorus and sulfur, and play a key role in maintaining soil carbon sink and ecosystem function. The study on effects of environmental and spatial factors on the structure of microbial community in boreal coniferous forest soil will provide theoretical basis for making management measures in local forest ecosystem. Our research analyzed five soil fungi communities (LpMC1, LpMC2, PwMC, PtMC, and BMC) in four forest types, including Larix principis-rupprechtii forest, Picea wilsonii forest, Pinus tabulaeformis forest and Betula spp. forest, respectively, in Pangquangou Nature Reserve in Guandi Mountains with Illumina high-throughput sequencing technology. Meanwhile, soil environmental factors and diversity of undergrowth plants were determined to analyze the relationship between fungi community structure and vegetation as well as soil environmental factors. The results showed that:①There were seven eumycota and thirty-three advantageous fungal genera in the five sample sites; ②Redundancy analysis results showed that soil pH, temperature, moisture, total nitrogen, the content of NH4+, total carbon, invertase activity, urease activity, undergrowth dominance and evenness were significantly associated with soil fungi community structure; ③Cluster analysis and principal component analysis showed that forest vegetation type, soil environmental factors and undergrowth had significant effects on soil fungi community structure; ④The results of PCNM analysis showed that at a local scale, dispersal limitation had no significant influence on fungi community structure in the study area. The forest soil fungi community structure in the study area was significantly affected by environmental selection (soil pH, temperature, moisture, total nitrogen, the content of NH4+, total carbon, invertase activity, urease activity, undergrowth dominance and evenness, forest type).

The effect of pH modification on wetting kinetics of a naturally water‐repellent coniferous forest soil

The interfacial dynamics of soil–water interactions are greatly affected by the hydrophobic properties of organic matter. The causes and underlying mechanisms responsible for the development of soil water repellency (SWR) are still under discussion. Various environmental factors control the appearance and degree of SWR. In addition to water content and temperature, the wetting of soil depends greatly on the physicochemical characteristics of soil surfaces, which in turn depend on pH. In this contribution, we propose a reaction mechanism for the change in SWR that is observed when soil pH is changed. Wetting kinetics were studied by time‐dependent sessile drop measurements (TISED) of the contact angle, the work of spreading and the diameter of the base of the drop as time elapsed under controlled relative humidity. Modification of pH strongly affected the wetting kinetics, suggesting maximum resistance to wetting at the control pH (3.6), with decreased resistance to wetting as pH was changed in either direction. The enhancement in wetting kinetics by the modification of soil pH can be attributed to the chemical modification in organic materials that coat the soil particles. This conclusion is based on the magnitude of activation energy associated with the spreading process. The combined effect of pH and temperature on the wetting kinetics, together with the compensation effect seen between the logarithmic pre‐exponential factor and activation energy, suggests acid–base catalysed hydrolysis–condensation reactions are the dominant processes responsible for the chemical nature of SWR.HighlightsHow does the modification of pH affect soil wetting mechanisms? The dynamic sessile drop method was used to measure the wetting activation energy. Modification of soil pH decreases resistance to wetting and increases activation energy of wetting. Acid or base catalysed hydrolysis reactions increase chemical sorption sites for water molecules in soil.

Soil methanotrophic community structure and diversity in different vegetation types at elevation gradient of Gongga Mountain, Southwest China

Methane (CH4) is the second abundant greenhouse gas. Aerobic methane oxidations of topsoil in forest are identified as an important sink of atmosphere methane, playing critical roles in carbon cycle and global warming alleviation. Comparing the community structure and diversity of methane oxidizing bacteria (MOBs) in different vegetation ecosystems could provide new insights into the relationships between vegetation types and community of MOBs. In this study, we collected 92 soil samples from four types of vegetation along the elevation gradient of Gongga Mountain, and further assessed the community structure, diversity and potential drivers of MOBs across the four vegetation types using Miseq sequencing and bioinformatics methods. The result indicated that MOBs community compositions in evergreen and deciduous broad-leaved forest (EDBF) and coniferous and broad-leaved mixed forest (CBMF) was more similar, whereas in dark coniferous forest (DCF) and shrub meadow area (SMA) soils, MOB composition was more similar. In the four types of vegetation, α-diversities of MOBs in EDBF and CBMF were significantly higher than that in the other three vegetation types (P＜0.001), whereas β-diversities in soils of DCF and SMA were significantly higher than those in EDBF and CBMF (P＜0.001). Spearman analysis indicated that the relative abundance of different MOBs in four types of vegetation showed different responses to environmental change. Factors including soil total nitrogen, conductivity and soil temperature appeared to govern the variation of α-diversity across the four vegetation types. Partial Mantel test and redundancy ana-lysis (RDA) suggested that environmental parameters likely contributed more to diversity variations in soils from EDBF and CBMF, whereas diversity variations in soils from DCF and SAM might be driven by other potential environmental factors or mechanism. Precipitation appeared to drive the β-diversity variation between vegetation of EDBF and CBMF and vegetation of DCF and SAM. Our study suggested that the community structure and diversity variation of MOBs in different vegetation types might be governed by both soil properties and climate change.

Effect of the Leaf Litter of Transgenic <i>Populus Simonii P. nigra</i> on the Soil Microbial Community and Horizontal Transfer Possibility of the Foreign Gene

To study the potential influence of transgenic Populus simonii×P. nigra on the soil microbial community composition and horizontal exogenous gene transfer, fresh transgenic leaves were treated in broadleaf and coniferous forest soil for 6 months in the laboratory. The results showed that DNA fragments of the target and marker genes were completely degraded before 120 days. The dominant colony is the bacterium whose number is much more than that of other microbes under the same treatment. The number of cultivable bacteria treated by transgenic litters was significantly higher than the number treated by non-transgenic litters in selective medium with kanamycin. The target gene in the entophytic and soil bacteria, with 1.92% and 3.08% PCR-positive results, was found only in broadleaf forest soil. This result showed a certain possibility of horizontal gene transfer from the transgenic poplar to soil bacteria.

Seasonal variation and distribution of total and active microbial community of β-glucosidase encoding genes in coniferous forest soil

Cellulose is the most abundant polysaccharide in the dead plant biomass, and its degradation is an important part of global carbon cycle. β-Glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. Genetic potential and expression of β-glucosidase genes were studied in the topsoil of a Picea abies forest in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families GH1 and GH3 amplified from DNA and RNA and amplicon pools were analyzed. Transcript pool were largely corresponded to gene pools, although some abundant transcripts were not found in the gene pool. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and Basidiomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria Acidobacteria and Deinococcus-Thermus. This indicates that a diverse microbial community utilized cellobiose. Seasonality influenced both genetic diversity of β-glucosidase genes and their expression. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in forest soils. Even β-glucosidase genes showing low abundance in DNA may be functionally important as revealed by their high expression especially in basidiomycota. The functional diversity in the studied ecosystem clearly exhibited a seasonal pattern.

PhytOC stock in forest litter in subtropical forests: Effects of parent material and forest type

Organic carbon (C) occluded in phytolith (PhytOC) is stable in the soil for millennia and can be an important contributor to long-term C storage in forest ecosystems. In order to understand the effect of parent material and vegetation type on the production of PhytOC in plant litter in subtropical forests in China, we investigated the PhytOC concentration and stock in plant litter in four forest types, moso bamboo (Phyllostachys edulis Moso), Chinese-fir (Cunninghamia lanceolata), evergreen broadleaf and mixed conifer-broadleaf forests, established on three parent materials (rhyolite, sandy shale and tuff). This study showed that: 1) both parent material and forest type significantly affected phytolith concentrations in litter, and there was a significant interaction between parent material and forest type. Plant litter in the moso bamboo forest developed on rhyolite and tuff had the highest phytolith concentrations followed by moso bamboo forest on sandy shale; 2) forest type but not parent material affected PhytOC concentrations in litter, with the highest in the moso bamboo forest; 3) both parent material and forest type significantly affected PhytOC stock in litter, without a significant interaction between the two factors. The moso bamboo forest had the highest PhytOC stock in its litter; and 4) the PhytOC stock returned to the soil in moso bamboo, Chinese-fir, evergreen broad-leaf and mixed coniferous forests was (mean±SD) 14.66±4.69, 2.87±2.19, 6.22±2.46 and 4.84±1.82kgha−1, respectively. Considering the area of the four respective forest types, the amount of C that can be entered into the soil in the form of PhytOC in litter was 2.08×105, 1.19×105, 5.68×105 and 2.75×104t CO2-e, respectively, and therefore it indicates a great potential in long-term C storage.

Litter input decreased the response of soil organic matter decomposition to warming in two subtropical forest soils.

Interaction effect of temperature and litter input on SOM decomposition is poor understood, restricting accurate prediction of the dynamics and stocks of soil organic carbon under global warming. To address this knowledge gap, we conducted an incubation experiment by adding 13C labeled leaf-litter into a coniferous forest (CF) soil and a broadleaved forest (BF) soil. In this experiment, response of the temperature sensitivity (Q10) of SOM decomposition to the increase in litter input was investigated. The temperature dependences of priming effect (PE) and soil microbial community were analyzed. The Q10 for CF soil significantly decreased from 2.41 in no-litter treatment to 2.05 in litter-added treatment and for BF soil from 2.14 to 1.82, suggesting that litter addition decreases the Q10. PE in the CF soil was 24.9% at 20 °C and 6.2% at 30 °C, and in the BF soil the PE was 8.8% at 20 °C and −7.0% at 30 °C, suggesting that PE decreases with increasing temperature. Relative PE was positively related to the concentrations of Gram-negative bacterial and fungal PLFAs. This study moves a step forward in understanding warming effect on forest carbon cycling by highlighting interaction effect of litter input and warming on soil carbon cycling.

Measurements of Boreal Coniferous Forest Soil and Humus With an Airborne Radiometer

Boreal coniferous forests are a large and diverse biome, which has not been widely studied in scope of space borne soil moisture (SM) observations. This paper presents a series of airborne measurements that were made to explore microwave emissivity of a boreal coniferous forest in different moisture conditions. Ground observations of SM and vegetation were made in conjunction with the airborne measurements. The L-band microwave emission of the biosphere (L-MEB) model, which is used in the SM and ocean salinity (SMOS) SM algorithm, was used to model the emission of the forest scenes. The litter layer was included in the modeling because of the thick humus layer present in the study area. The measurements indicate that with sufficient parameters the L-MEB model can simulate the forest and soil-humus ensemble emission with reasonable accuracy ( ${\text{R}} = 0.75$ , ${\text{RMSE}} = 4.4{\text{ K}}$ ). While SM retrieval is hampered by the complex behavior of humus layer, a correct parameterization of the layer is likely to improve accuracy of moisture retrieval for mixed pixels in SMOS observations.

Chlorination and dechlorination rates in a forest soil — A combined modelling and experimental approach

Much of the total pool of chlorine (Cl) in soil consists of naturally produced organic chlorine (Clorg). The chlorination of bulk organic matter at substantial rates has been experimentally confirmed in various soil types. The subsequent fates of Clorg are important for ecosystem Cl cycling and residence times. As most previous research into dechlorination in soils has examined either single substances or specific groups of compounds, we lack information about overall bulk dechlorination rates. Here we assessed bulk organic matter chlorination and dechlorination rates in coniferous forest soil based on a radiotracer experiment conducted under various environmental conditions (additional water, labile organic matter, and ammonium nitrate). Experiment results were used to develop a model to estimate specific chlorination (i.e., fraction of Cl− transformed to Clorg per time unit) and specific dechlorination (i.e., fraction of Clorg transformed to Cl− per time unit) rates. The results indicate that chlorination and dechlorination occurred simultaneously under all tested environmental conditions. Specific chlorination rates ranged from 0.0005 to 0.01 d−1 and were hampered by nitrogen fertilization but were otherwise similar among the treatments. Specific dechlorination rates were 0.01–0.03d−1 and were similar among all treatments. This study finds that soil Clorg levels result from a dynamic equilibrium between the chlorination and rapid dechlorination of some Clorg compounds, while another Clorg pool is dechlorinated more slowly. Altogether, this study demonstrates a highly active Cl cycling in soils.

Small scale temporal distribution of radiocesium in undisturbed coniferous forest soil: Radiocesium depth distribution profiles

The depth distribution of pre-Fukushima and Fukushima-derived 137Cs in undisturbed coniferous forest soil was investigated at four sampling dates from nine months to 18 months after the Fukushima nuclear power plant accident. The migration rate and short-term temporal variability among the sampling profiles were evaluated. Taking the time elapsed since the peak deposition of pre-Fukushima 137Cs and the median depth of the peaks, its downward displacement rates ranged from 0.15 to 0.67 mm yr−1 with a mean of 0.46 ± 0.25 mm yr−1. On the other hand, in each examined profile considerable amount of the Fukushima-derived 137Cs was found in the organic layer (51%–92%). At this moment, the effect of time-distance on the downward distribution of Fukushima-derived 137Cs seems invisible as its large portion is still found in layers where organic matter is maximal. This indicates that organic matter seems the primary and preferential sorbent of radiocesium that could be associated with the physical blockage of the exchanging sites by organic-rich dusts that act as a buffer against downward propagation of radiocesium, implying radiocesium to be remained in the root zone for considerable time period. As a result, this soil section can be a potential source of radiation dose largely due to high radiocesium concentration coupled with its low density. Generally, such kind of information will be useful to establish a dynamic safety-focused decision support system to ease and assist management actions.

Silvibacterium bohemicum gen. nov. sp. nov., an acidobacterium isolated from coniferous soil in the Bohemian Forest National Park

During the course of a study assessing the bacterial diversity of a coniferous forest soil (pH 3.8) in the Bohemian Forest National Park (Czech Republic), we isolated strain S15T which corresponded to one of the most abundant soil OTUs. Strain S15T is represented by Gram-negative, motile, rod-like cells that are 0.3–0.5μm in diameter and 0.9–1.1μm in length. Its pH range for growth was 3–6, with optimal conditions found at approximately 4–5. It can grow at temperatures between 20°C and 28°C, with optimum growth at 22–24°C. Its respiratory quinone is MK-8, and its main fatty acid is iso-C15:0 (73.7%). The G+C DNA content was 58.2mol%. According to the 16S rRNA gene sequence analysis, strain S15T belongs to subdivision 1 of the phylum Acidobacteria, being affiliated to the cluster of Acidipila rosea AP8T and Acidobacterium capsulatum ATCC 51196T. Analysis of the S15T genome revealed the presence of 404 genes that are involved in carbohydrate metabolism, which indicates the metabolic potential to degrade polysaccharides of plant and fungal origin. Based on genotypic and phenotypic characteristics, the strain S15T represents a new genus and species within the family Acidobacteriaceae, for which the name Silvibacterium bohemicum gen. nov., sp. nov. is proposed (type strain S15T=LMG 28607T=CECT 8790T).

Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation.

Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55(T), which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55(T) include Bryocella elongata SN10(T) (95.4% identity), Acidicapsa ligni WH120(T) (95.2% identity), and Telmatobacter bradus TPB6017(T) (95.0% identity), revealing that strain S55(T) should be classified within the phylum Acidobacteria, subdivision 1. Strain S55(T) is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55(T) corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55(T) = NBRC 111238(T) = CECT 8791(T)). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55(T) also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55(T) being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55(T) in the carbon cycle in the Picea abies coniferous forest.

Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition

Coniferous forest soils have an indispensable ecological role in the global cycles of nutrients on Earth. Despite the fact that microbial communities in this ecosystem were subject of multiple studies, the involvement of individual taxa in the processes of organic matter transformation and the functional roles of dominant and active bacteria are largely unknown. Here, we have performed a comprehensive isolation effort to obtain multiple dominant bacterial taxa from a Picea abies forest soil and provide their physiological characterization. This information allows us to link ecological traits with groups of microorganisms. In the study, conventional culture techniques at acidic pH and low-nutrient content led to the recovery of 299 bacterial isolates. The isolates represented operational taxonomic units (OTUs) that contained 20 and 32 % of all bacterial genomes detected in the litter and soil by 16S amplicon analysis, including some of those bacterial strains representing the most abundant and active OTUs. These included also several isolates of the still underexplored phylum of the Acidobacteria, all of them belonging to the subdivision 1 of the phylum. Acidobacterial isolates produced the widest range of enzymes among all isolates and highest enzyme activities in acidic conditions. Moreover, members of the Acidobacteria represented more than 50 % of the isolates able to grow on disaccharides produced during the breakdown of cellulose, chitin, and starch. Our results indicate that Acidobacteria may play an important ecological role by degrading polysaccharides of plant and fungal origin in the important ecosystems of acidic coniferous forests.

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter.

Understanding the ecology of coniferous forests is very important because these environments represent globally largest carbon sinks. Metatranscriptomics, microbial community and enzyme analyses were combined to describe the detailed role of microbial taxa in the functioning of the Picea abies-dominated coniferous forest soil in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. The results show that microbial communities were characterized by a high activity of fungi especially in litter where their contribution to microbial transcription was over 50%. Differences in abundance between summer and winter were recorded for 26-33% of bacterial genera and < 15% of fungal genera, but the transcript profiles of fungi, archaea and most bacterial phyla were significantly different among seasons. Further, the seasonal differences were larger in soil than in litter. Most importantly, fungal contribution to total microbial transcription in soil decreased from 33% in summer to 16% in winter. In particular, the activity of the abundant ectomycorrhizal fungi was reduced in winter, which indicates that plant photosynthetic production was likely one of the major drivers of changes in the functioning of microbial communities in this coniferous forest.

Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils.

Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils.

The genus Bradyrhizobium has served as a model system for studying host-microbe symbiotic interactions and nitrogen fixation due to its importance in agricultural productivity and global nitrogen cycling. In this study, we identify a bacterial group affiliated with this genus that dominates the microbial communities of coniferous forest soils from six distinct ecozones across North America. Representative isolates from this group were obtained and characterized. Using quantitative population genomics, we show that forest soil populations of Bradyrhizobium represent ecotypes incapable of nodulating legume root hairs or fixing atmospheric nitrogen. Instead, these populations appear to be free living and have a greater potential for metabolizing aromatic carbon sources than their close symbiotic relatives. In addition, we identify fine-scaled differentiation between populations inhabiting neighboring soil layers that illustrate how diversity within Bradyrhizobium is structured by habitat similarity. These findings reconcile incongruent observations about this widely studied and important group of bacteria and highlight the value of ecological context to interpretations of microbial diversity and taxonomy. These results further suggest that the influence of this genus likely extends well beyond facilitating agriculture, especially as forest ecosystems are large and integral components of the biosphere. In addition, this study demonstrates how focusing research on economically important microorganisms can bias our understanding of the natural world.

Exploring the activity of microorganisms in the forest soil using metatranscriptomics

Metatranscriptomics combined with microbial community analysis was used to describe the roles of individual microbial taxa in the coniferous forest soil in two contrasting seasons. Both the microbial community composition and the pool of microbial transcripts were found to be highly diverse and subject to seasonal changes, especially in soil.