Land use and climatic factors structure regional patterns in soil microbial communities

Aim  Although patterns are emerging for macroorganisms, we have limited understanding of the factors determining soil microbial community composition and productivity at large spatial extents. The overall objective of this study was to discern the drivers of microbial community composition at the extent of biogeographical provinces and regions. We hypothesized that factors associated with land use and climate would drive soil microbial community composition and biomass.
Location  Great Basin Province, Desert Province and California Floristic Province, California, USA.
Methods  Using phospholipid fatty acid analysis, we compared microbial communities across eight land-use types sampled throughout the State of California, USA ( n = 1117).
Results  The main factor driving composition and microbial biomass was land-use type, especially as related to water availability and disturbance. Dry soils were more enriched in Gram-negative bacteria and fungi, and wetter soils were more enriched in Gram-positive, anaerobic and sulphate-reducing bacteria. Microbial biomass was lowest in ecosystems with the wettest and driest soils. Disturbed soils had less fungal and more Gram-positive bacterial biomass than wildland soils. However, some factors known to influence microbial communities, such as soil pH and specific plant taxa, were not important here.
Main conclusions  Distinct microbial communities were associated with land-use types and disturbance at the regional extent. Overall, soil water availability was an important determinant of soil microbial community composition. However, because of the inclusion of managed and irrigated agricultural ecosystems, the effect of precipitation was not significant. Effects of environmental and management factors, such as flooding, tillage and irrigation, suggest that agricultural management can have larger effects on soil microbial communities than elevation and precipitation gradients.     

Burning Fire-Prone Mediterranean Shrublands: Immediate Changes in Soil Microbial Community Structure and Ecosystem Functions

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.     

Spatial and Temporal Variation of Archaeal,Bacterial and Fungal Communities in Agricultural Soils

Background

Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

Methodology/Principal Findings

In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

Conclusions

Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.     

Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome

The Pampa biome is considered one of the main hotspots of the world’s biodiversity and it is estimated that half of its original vegetation was removed and converted to agricultural land and tree plantations. Although an increasing amount of knowledge is being assembled regarding the response of soil bacterial communities to land use change, to the associated plant community and to soil properties, our understanding about how these interactions affect the microbial community from the Brazilian Pampa is still poor and incomplete. In this study, we hypothesized that the same soil type from the same geographic region but under distinct land use present dissimilar soil bacterial communities. To test this hypothesis, we assessed the soil bacterial communities from four land-uses within the same soil type by 454-pyrosequencing of 16S rRNA gene and by soil microbial activity analyzes. We found that the same soil type under different land uses harbor similar (but not equal) bacterial communities and the differences were controlled by many microbial taxa. No differences regarding diversity and richness between natural areas and areas under anthropogenic disturbance were detected. However, the measures of microbial activity did not converge with the 16S rRNA data supporting the idea that the coupling between functioning and composition of bacterial communities is not necessarily correlated.     

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations.     

Organic Layer Serves as a Hotspot of Microbial Activity and Abundance in Arctic Tundra Soils

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.     

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO₂ given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short‐term effects of wildfire to the long‐term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both ¹³C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition.     

Biogeographic responses and niche occupancy of microbial communities following long-term land-use change

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world’s largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself.

     

Soil textural class plays a major role in evaluating the effects of land use on soil quality indicators

Inappropriate land use that negatively affects ecological processes and soil quality is generally considered to be the primary cause of soil degradation in tropical agroecosystems. We hypothesized that in addition to land use, soil textural class also has an important effect on ecological processes and soil quality. To test our hypothesis, effects of land use change on soil organic fractions as well as microbial and biochemical indicators were quantified for clayey and sandy-clay-loam soils within the native Cerrado biome, pasture (Brachiaria brizantha) and sugarcane (Saccharum officinarum) agroecosystems in southwestern Brazil (Minas Gerais state). Labile carbon, humic substances, soil microbial respiration (SMR), microbial biomass carbon (MBC), metabolic quotient (qCO₂), hydrolysis of fluorescein diacetate (FDA), beta-glucosidase, urease, phosphatase and arylsulphatase activities were measured for each sample. Labile carbon concentrations were not affected by land use but were lower in sandy-clay-loam soil than clayey soil. Humic substances were at the highest concentrations in the native Cerrado and the lowest in sugarcane agroecosystems. Sandy-clay-loam soil had lower humic acid concentrations than clayey soil. Soil microbial indicators (SMR, MBC and FDA) showed lower values in pasture and sugarcane agroecosystems than in the native Cerrado. FDA was a more sensitive microbial indicator than SMR and MBC for detecting land use and textural class differences. The qCO₂ indices were greater in sugarcane systems than in either pasture or native Cerrado systems. The activity of exocellular hydrolytic enzymes, such as beta-glucosidase, urease, phosphatase and arylsulphatase, was smaller in sugarcane and pasture agroecosystems than in native Cerrado ecosystems. Within the same land use, the activity of these enzymes was always greater in clayey soil than in sandy-clay-loam soil, indicating a higher impact of land uses on enzyme activities in clayey soils. Results for the measured indicators support the hypothesis that soil textural class plays a major role in assessing differences between land use systems in the Brazilian Cerrado biome.     

Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.     

Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.     

水田改果园后土壤性质的变化及其特征

近年来,水田改作经济林地,在我国南方地区非常普遍。为深入了解这一转变对土壤质量的影响,以浙江省典型水稻土(青粉泥田)及其改果园不同年限的系列表层土壤(0—15 cm)为研究对象,应用磷脂脂肪酸生物标记等方法,研究了水田改果园后土壤理化性质和微生物群落结构等性质的变化以及它们之间的关系。结果表明,水田改果园后,土壤中大于0.25 mm水稳定性团聚体、盐基饱和度、p H值、有机质、全氮和碱解氮等随着改果园年限的延长而显著降低(P0.05)。土壤微生物生物量碳氮、微生物商和土壤呼吸强度随改果园年限增加而显著下降(P0.01)。土壤微生物群落结构也发生明显变化:磷脂脂肪酸总量显著降低(P0.01),微生物种类减少,原生动物在土壤微生物中所占比例增加,革兰氏阴性细菌与革兰氏阳性细菌比值降低(P0.01),好氧细菌/厌氧细菌和甲烷氧化菌/细菌增加(P0.01),表征养分胁迫的环丙基脂肪酸/前体物和异式脂肪酸/反异支链脂肪酸显著增加(P0.01)。冗余分析表明,土壤含水率、有机质和碱解氮是决定水田和果园土壤微生物群落结构差异的最重要因子(P0.01);改果园后,土壤微生物群落结构发生了阶段性变化,不同利用方式对微生物群落结构的影响程度要大于同一利用方式耕作不同年限对微生物群落结构的影响。研究表明,水田改果园后土壤理化性质以及生物学性质发生退化,土壤质量下降;而水田中微生物数量和种类都比较丰富,因而认为水田是土壤(地)可持续利用的一种有效方式。     

Distinct microbial communities associated with buried soils in the Siberian tundra

Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.     

Size, activity and catabolic diversity of the soil microbial biomass in a wetland complex invaded by reed canary grass

Reed canary grass (Phalaris arundinacea, L.) invasion of wetlands is an ecological issue that has received attention, but its impact on soil microbial diversity is not well documented. The present study assessed the size (substrate-induced respiration), catabolic diversity (CLPP, community level physiological profiles) and composition (selective inhibition) of the soil microbial community in invaded (>95% P. arundinacea cover) and in non-invaded areas of a wetland occupied by native species grown either as a mixed assemblage (22 species) or as quasi-monotypic stands of Scirpus cyperinus (74% cover). The study also tested the hypothesis that decomposition of lignin- and phenolics-rich plant tissues would be fastest in soils exhibiting high catabolic diversity. Results showed that soil respiration, microbial biomass and diversity were significantly higher (P?<?0.03; 1.5 to 3 fold) in P. arundinacea-invaded soils than in soils supporting native plant species. Fungal to bacterial ratios were also higher in invaded (0.6) than in non-invaded (0.4) plots. Further, canonical discriminant analysis of CLPP data showed distinct communities of soil decomposers associated with each plant community. However, these differences in microbial attributes had no effect on decomposition of plant biomass which was primarily controlled by its chemical composition. While P. arundinacea invasion has substantially reduced plant diversity, this study found no parallel decline in the size and diversity of the soil microbial community in the invaded areas.     

Microbial quality of soil from the Pampa biome in response to different grazing pressures

The aim of this study was to evaluate the impact of different grazing pressures on the activity and diversity of soil bacteria. We performed a long-term experiment in Eldorado do Sul, southern Brazil, that assessed three levels of grazing pressure: high pressure (HP), with 4% herbage allowance (HA), moderate pressure (MP), with 12% HA, and low pressure (LP), with 16% HA. Two reference areas were also assessed, one of never-grazed native vegetation (NG) and another of regenerated vegetation after two years of grazing (RG). Soil samples were evaluated for microbial biomass and enzymatic (β-glucosidase, arylsulfatase and urease) activities. The structure of the bacterial community and the population of diazotrophic bacteria were evaluated by RFLP of the 16S rRNA and nifH genes, respectively. The diversity of diazotrophic bacteria was assessed by partial sequencing of the 16S rDNA gene. The presence of grazing animals increased soil microbial biomass in MP and HP. The structures of the bacterial community and the populations of diazotrophic bacteria were altered by the different grazing managements, with a greater diversity of diazotrophic bacteria in the LP treatment. Based on the characteristics evaluated, the MP treatment was the most appropriate for animal production and conservation of the Pampa biome.     

Contrasting diurnal variations in soil organic carbon decomposition and root respiration due to a hysteresis effect with soil temperature in a Gossypium s. (cotton) plantation

Cool-season grasses commonly harbor fungal endophytes in their aerial tissues. However the effects of these symbionts on soil microbial communities have rarely been investigated. Our objective was to explore microbial community responses in soils conditioned by plants of the annual grass Lolium multiflorum with contrasting levels of infection with the endophyte Neotyphodium occultans. At the end of the host growing season, we estimated the functional capacity of soil microbial communities (via catabolic response profiles), the contribution of fungi and bacteria to soil activity (via selective inhibition with antibiotics), and the structure of both microbial communities by molecular analyses. Soil conditioning by highly infected plants affected soil catabolic profiles and tended to increase soil fungal activity. We detected a shift in bacterial community structure while no changes were observed for fungi. Soil responses became evident even without changes in host plant biomass or soil organic carbon or total nitrogen content, suggesting that the endophyte modified host rhizodepositions during the conditioning phase. Our results have implications for the understanding of the reciprocal interactions between above and belowground communities, suggesting that plant-soil feedbacks can be mediated by this symbiosis.     

Soil microbial properties under different vegetation types on Mountain Han

This study investigated the influence of broadleaf and conifer vegetation on soil microbial communities in a distinct vertical distribution belt in Northeast China.Soil samples were taken at 0-5,5-10 and 10-20 cm depths from four vegetation types at different altitudes,which were characterized by poplar(Populus davidiana)(1250-1300 m),poplar(P.davidiana) mixed with birch(Betula platyphylla)(1370-1550 m),birch(B.platyphylla)(1550-1720 m),and larch(Larix principis-rupprechtii)(1840-1890 m).Microbial biomass and community structure were determined using the fumigation-extraction method and phospholipid fatty acid(PLFA) analysis,and soil fungal community level physiological profiles(CLPP) were characterized using Biolog FF Microplates.It was found that soil properties,especially soil organic carbon and water content,contributed significantly to the variations in soil microbes.With increasing soil depth,the soil microbial biomass,fungal biomass,and fungal catabolic ability diminished;however,the ratio of fungi to bacteria increased.The fungal ratio was higher under larch forests compared to that under poplar,birch,and their mixed forests,although the soil microbial biomass was lower.The direct contribution of vegetation types to the soil microbial community variation was 12%.If the indirect contribution through soil organic carbon was included,variations in the vegetation type had substantial influences on soil microbial composition and diversity.     

The importance of amino sugar turnover to C and N cycling in organic horizons of old-growth Douglas-fir forest soils colonized by ectomycorrhizal mats

Amino sugar dynamics represent an important but under-investigated component of the carbon (C) and nitrogen (N) cycles in old-growth Douglas-fir forest soils. Because fungal biomass is high in these soils, particularly in areas colonized by rhizomorphic ectomycorrhizal fungal mats, organic matter derived from chitinous cell wall material (or the monomeric building block of chitin, N-acetylglucosamine (NAG)) could be a significant source of C or N to the soil microbiota, and thus an important driver of microbial C and N processing. This paper reports the results of incubation experiments initiated to measure chitin degradation, NAG utilization, and the contribution of these substrates to soil respiration and N mineralization rates in mat-colonized and non-mat soil organic horizons. Amendments of chitin and NAG stimulated respiration, N mineralization, and biomass accumulation in mat and non-mat soils, and responses to NAG amendment were stronger than to chitin amendment. NAG-induced respiration was consistently two-fold higher in mat soils than non-mat soils, but induced N mineralization was similar between the two soil patch types. Assimilation of both C and N into microbial biomass was apparent, biomass C:N ratio decreased in all treatments, and microbial N use efficiency (treatment means 0.25 ± 0.06–0.50 ± 0.05) was greater than C use efficiency (treatment means 0.12 ± 0.04–0.32 ± 0.02). NAGase enzyme response was non-linear and showed the same pattern in chitin and NAG amendments. Responses to NAG and chitin amendment differed between mat and non-mat soils, indicating different mechanisms driving NAG and chitin utilization or differences in saprotrophic community composition between the two soil patch types. Net chitin and NAG processing rates were 0.08–3.4 times the basal respiration rates and 0.07–14 times the ambient net N mineralization rates, high enough for the turnover of total soil amino sugars to potentially occur in days to weeks. The results support the hypotheses that amino sugars are important microbial C and N sources and drivers of C and N cycling in these soils.     

Microbial community biogeographic patterns in the rhizosphere of two Brazilian semi-arid leguminous trees

Arid environments are regular and well distributed over all continents and display drought characteristics whether full-time or seasonal. This study aims to characterize how the microbial communities of the rhizosphere of two leguminous trees from the Brazilian semi-arid biome the Caatinga are geographically and seasonally shaped, as well as the factors driving this variation. With that purpose, the soil rhizosphere from two leguminous trees (Mimosa tenuiflora and Piptadenia stipulacea (Benth.) Ducke) were sampled in two different seasons: rainy and drought at five different sites. Assessment of bacterial and archaeal communities occurred by T-RFLP analysis of 16S rRNA and archaeal amoA genes. By these means, it was observed that the seasons (wet and dry periods) are the factors that most influence the composition of the microbial community from both analyzed plants, except for the results obtained from the CCA applied to Archaeas. Furthermore, soil physical–chemical factors also had a significant influence on the community and indicated a geographical pattern of the bacterial community. It was not possible to observe significant modifications in the composition in relation to the plant species. We have seen that soil characteristics and rainfall were the factors that most influenced the microbial composition. Also, the bacterial community had a significant correlation with soil characteristics that indicates that these rhizosphere communities might be selected by environmental characteristics. Furthermore, the data suggest that climate plays a key role in structuring the microbial community of this biome.     

Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods

In many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. The nirK gene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart, nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.