Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled from the Ljubljana Marsh under different seasonal conditions. Substrate-induced respiration and dehydrogenase activity were used as indicators of total microbial activity. Both methods indicated higher microbial activities in the fen soil with the higher SOC content on all dates of sampling. To determine whether the differences in microbial activity were associated with differences in the microbial community structures, terminal restriction fragment length polymorphism (T-RFLP) of bacterial 16S rRNA genes was performed. Comparison of the T-RFLP profiles revealed very similar community structures in both fens and in the two seasonal extremes investigated. This suggested a stable community structure in the two fens, which is not affected by the SOC content or seasonal variation. In addition, a bacterial 16S ribosomal RNA gene based clone library was prepared from the fen soil with the higher SOC content. Out of 114 clones analysed, approximately 53% belonged to the Proteobacteria, 23% to the Acidobacteria, 21% to a variety of other taxa, and less than 3% were affiliated with the Firmicutes.     

Impact of sulfadiazine and chlorotetracycline on soil bacterial community structure and respiratory activity

Veterinary medicines enter agricultural soils by the use of animal excrements as fertilizers. To study their impact on soil bacterial communities, microcosms containing orthic luvisol soil were spiked with the antimicrobial agents sulfadiazine (SDZ) and chlorotetracycline (CTC) at three different concentrations (1, 10, 50 mg kg⁻¹ soil) and incubated for 48 days at 20 °C. The impact on the microbial respiratory activity was measured continuously in a respirometer (Sapromat). Changes in bacterial community structure were visualized by means of PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA derived from soil samples after 1, 7, 11 and 48 days. Additionally, growth inhibitory effects of SDZ and CTC on bacteria previously isolated from the same soil were tested in agar diffusion tests. In microcosms with soil and antibiotics only, no effects could be observed, either on respiratory activity or on bacterial population structure. Therefore, further incubations were conducted in the presence of an additional assimilable carbon source (5 g glucose kg⁻¹ soil). In the presence of glucose, SDZ affected soil respiration as well as the bacterial community structure: Additional bands appeared and some bands already visible at the beginning of incubations increased in intensity. A clear relationship between SDZ concentrations and changes in DGGE patterns became visible. During 48 days of incubation, changes in DGGE patterns were minimal in microcosms with 50 mg SDZ kg⁻¹soil indicating an inhibition of strains, which were capable of growing on glucose in the presence of lower SDZ concentrations. Only a few soil bacterial isolates (5 out of 47 strains tested) were weakly inhibited by SDZ in agar diffusion disk tests. Contrastingly, CTC inhibited growth of 12 soil bacterial isolates significantly in disk tests, but no effects on soil respiration and bacterial community structure could be observed. In the presence of the soil matrix the growth inhibitory potential of CTC decreased due to adsorption or complexation. This was confirmed in growth inhibition experiments with soil suspensions and time-dependent sampling.     

Bacterial community structure and microbial activity in different soils amended with biogas residues and cattle slurry

Anaerobic digestion of organic materials generates residues of differing chemical composition compared to undigested animal manures, which may affect the soil microbial ecosystem differently when used as fertilizers. This study investigated the effects of two biogas residues (BR-A and BR-B) and cattle slurry (CS) applied at rates corresponding to 70 kg NH₄⁺-N ha⁻¹ on bacterial community structure and microbial activity in three soils of different texture (a sandy, a clay and an organic clay soil). 16S rRNA genes were targeted in PCR reactions and bacterial community profiles visualized using terminal restriction fragment length polymorphism. General microbial activity was measured as basal respiration (B-resp), substrate-induced respiration (SIR), specific growth rate (μ_SIR), metabolic quotient (qCO₂) and nitrogen mineralization capacity (NMC). Non-metric multidimensional scaling analysis visualized shifts in bacterial community structure related to microbial functions. There were significant differences in bacterial community structure after 120 days of incubation (+20 °C at 70% of WHC) between non-amended (control) and amended soils, especially in the sandy soil, where CS caused a more pronounced shift than biogas residues. Terminal-restriction fragment (TRF) 307, the predominant peak in CS-amended sandy soil, was identified as possibly Bacillus or Streptococcus. TRF 226, the dominant peak in organic soil amended with BR-B, was classified as Rhodopseudomonas. B-resp significantly increased and SIR decreased in all amendments to organic soil compared with the control, potentially indicating decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass. This was also reflected in an elevated qCO₂ in the organic soil. The μ_SIR level was higher in the sandy soil amended with BR-A than with BR-B or CS, indicating a shift toward species capable of rapidly utilizing glucose. NMC was significantly elevated in the clay and organic soils amended with BR-A and BR-B and in the sandy soil amended with BR-B and CS. Thus, biogas residues and cattle slurry had different effects on the bacterial community structure and microbial activity in the three soils. However, the effects of biogas residues on microbial activities were comparable in magnitude to those of cattle slurry and the bacterial community structure was less affected. Therefore, we do not see any reason not to recommend using biogas residues as fertilizers based on the results presented.     

Methyl-mercury affects microbial activity and biomass,bacterial community structure but rarely the fungal community structure

Monomethyl-mercury is one of the most toxic compounds. Methylation of Hg usually appears under anoxic conditions. In Swiss forest soils, methyl-Hg concentrations of up to 3 μg kg⁻¹ soil dw have been observed, but the impact of methyl-Hg on soil microorganisms have rarely been examined so far. In this study, we investigated the effect of increasing concentrations of methyl-Hg (0, 5, 20, 90 μg kg⁻¹ soil dw) on the microbial communities in various forest soils differing in their physico-chemical properties. Experiments were conducted in microcosms under controlled conditions and the basal respiration (BR), the microbial biomass carbon (MBC) and the bacterial and fungal community structures using T-RFLP-profiling were investigated. BR was significantly affected by methyl-Hg. In general, the BR increased with increasing methyl-Hg concentrations, whereas the MBC was significantly reduced. Bacterial communities were more sensitive to methyl-Hg than fungal communities. In five out of seven soils, the bacterial community structures differed significantly between the treatments whereas the fungal communities did not. The impact of methyl-Hg on the soil bacterial communities was site specific. In one soil, a methyl-Hg concentration of already 5 μg kg⁻¹ soil dw significantly affected the relative abundance of 13% bacterial operational taxonomic units (OTU), whereas in other soils concentrations of even 90 μg kg⁻¹ soil dw rarely affected the abundance of OTUs. In this study, for the first time, the impact of methyl-Hg on soil bacterial and fungal communities in forest soils was assessed. We showed that its impact strongly depends on the physico-chemical conditions of the soil and that bacterial communities were more sensitive to methyl-Hg than fungi.     

盐地碱蓬根际土壤细菌群落结构及其功能

盐地碱蓬作为生物改良盐碱地的理想材料,其根际土壤微生物对土壤改良发挥着重要作用。为了深入探索环渤海滨海盐碱地碱蓬根际土壤细菌群落结构组成及其功能,采用Illumina Misep高通量测序平台对环渤海地区滨海盐碱地盐地碱蓬根际土壤和裸地土壤进行测序。从16个样本中获得有效序列734 792条, 4 285个OTUs,归属于41门、100纲、282目、400科、892属、1 577种。盐地碱蓬根际土壤细菌群落由变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、绿弯曲门(Chloroflexi)、拟杆菌门(Bacteroidetes)、芽单胞菌门(Gemmatimonadetes)、酸杆菌门(Acidobacteria)、厚壁菌门(Firmicutes)、蓝藻细菌门(Cyanobacteria)、髌骨细菌门(Patescibacteria、浮霉菌门(Planctomycetes)组成。Alpha多样性计算结果表明,盐地碱蓬根际土壤细菌群落结构多样性高并与裸地土壤间差异显著;LEfSe(LDAEffectSize)分析发现,盐地碱蓬与裸地差异指示种明显不同。PCoA与相关性Heatmap表明,盐地碱蓬、速效氮、速效钾、速效磷、电导率是影响土壤细菌目类水平群落组成的主要因子。PICRUSt(Phylogenetic InvestigationofCommunitiesbyReconstructionofUnobserved States)分析表明微生物群落在新陈代谢等40个功能方面盐地碱蓬根际土壤比裸地土壤高。本研究表明盐地碱蓬覆盖能够降低土壤盐分,增加土壤养分,对土壤细菌群落多样性及其功能有积极作用。     

Compaction of forest soils with heavy logging machinery affects soil bacterial community structure

Soil compaction is widespread but tends to be most prevalent where heavy machinery is used in landfill sites, agriculture and forestry. Three forest sites strongly disturbed by heavy logging machinery were chosen to test the physical effects of different levels of compaction on soil bacterial community structure and soil functions. Community analysis comprised microbial biomass C and T-RFLP genetic profiling. Machine passes, irrespective of the compaction level, considerably modified soil structural characteristics at two soil depths (5–10 cm; 15–20 cm). Total porosity decreased up to 17% in the severe compaction. Reflected in this overall decline were large decreases in macroporosity (>50 μm). Reduction in macroporosity was associated with higher water retention and restricted gas exchange in compacted soils. The strongest effect was observed in the severely compacted wheel tracks where air and water conductivities were reduced permanently to 10% or even lower of the original conductivities of undisturbed soils. Very slow drainage in combination with a dramatically reduced gas permeability led to unfavorable soil conditions in severely disturbed traffic lanes reflecting the changes in the total bacterial community structures at both soil depths. Additionally, microbial biomass C tended to be lower in compacted soil. Our results indicate that the type of severe treatments imposed at these forest sites may have strong adverse effects on long-term soil sustainability.     

Clear-cutting affects the ammonia-oxidising community differently in limed and non-limed coniferous forest soils

The effects of clear-cutting on the ammonia-oxidising bacterial community were studied in the soil of limed and non-limed spruce forest plots located in the central part of southern Sweden. The communities were studied using denaturing gradient gel electrophoresis (DGGE) profiling after polymerase chain reaction (PCR) amplification from total DNA with primers reported to be specific for -subgroup ammonia-oxidising bacteria. The bands on the DGGE were sequenced and each unique sequence was interpreted as representing one ammonia-oxidising population. The relative abundance of each population was determined by measuring the fluorescence of the respective DGGE bands. In both limed and non-limed soil, the same two Nitrosospira populations were found, one belonging to cluster 2 (NScl2) and one to cluster 4 (NScl4). However, while NScl4 first appeared a year after the clear-cutting in the non-limed plot, it was present both before and after the cutting in the limed plot. Irrespective of previous liming, clear-cutting caused a shift in the ammonia-oxidiser community, from dominance by the NScl2 population to a community with approximately equal relative abundance of NScl2 and NScl4. In both plots the total size of the community increased after clear-cutting (based on increased DGGE band intensity), most likely due to increased NH₄⁺ availability, but the growth response was faster in the limed plot. Hence, the prior liming increased the responsiveness of the ammonia-oxidisers to the changes caused by cutting. This is the first study to report the effects of clear-cutting on the ammonia-oxidising community, and the results show a clear correlation between increased potential nitrification and a shift in the ammonia-oxidiser community.     

连作对再植枸杞根际细菌群落多样性和群落结构的影响研究

受枸杞道地产区土地资源等因素限制,连作障碍已成为影响枸杞产业发展的重要原因之一,导致严重的经济损失.研究连作条件下枸杞农田土壤生态系统微生物群落的演替规律对枸杞产业的可持续发展具有重要的理论意义.以宁夏银川市南梁农场连作多年的枸杞地为研究对象,利用Illumina MiSeq测序技术分析了连作对再植枸杞根际/非根际细菌群落的影响.结果表明,连作地显著抑制再植枸杞苗地径的增加,且其土壤pH较对照样地显著降低(p<0.05).测序结果证实,与对照样地相比,连作地再植枸杞根际土壤细菌物种数显著降低(p<0.05),细菌群落α多样性下降(p>0.05).主坐标分析表明,连作和对照样地间枸杞非根际细菌群落结构无明显差异,但连作显著改变再植枸杞根际细菌的群落结构.对细菌群落丰度的统计分析发现,连作地枸杞根际浮霉菌门、非根际假单胞菌门的相对丰度较对照样地显著降低(p<0.05).此外,冗余分析结果表明:枸杞园土壤pH和有效磷含量是影响枸杞非根际土壤细菌群落结构变化的主要因素,分别解释了41.8%和35.4%的群落结构变化(p<0.05),其他土壤因子无统计学意义,但土壤理化因子对再植枸杞根际细菌群落结构变化的影响均未达显著水平.这些结果证实连作能够显著抑制再植枸杞生长、影响再植枸杞根际细菌群落结构和多样性,干扰枸杞与土壤细菌群落间的互作关系.这些研究结果将为解析枸杞连作障碍机制提供理论基础.     

Microbial activity and community structure of a soil after heavy metal contamination in a model forest ecosystem

We assessed the effects of chronic heavy metal (HM) contamination on soil microbial communities in a newly established forest ecosystem. We hypothesized that HM would affect community function and alter the microbial community structure over time and that the effects are more pronounced in combination with acid rain (AR). These hypotheses were tested in a model forest ecosystem consisting of several tree species (Norway spruce, birch, willow, and poplar) maintained in open top chambers. HMs were added to the topsoil as filter dust from a secondary metal smelter and two types of irrigation water acidity (ambient rain vs. acidified rain) were applied during four vegetation periods. HM contamination strongly impacted the microbial biomass (measured with both fumigation-extraction and quantitative lipid biomarker analyses) and community function (measured as basal respiration and soil hydrolase activities) of the soil microbial communities. The most drastic effect was found in the combined treatment of HM and AR, although soil pH and bioavailable HM contents were comparable to those of treatments with HM alone. Analyses of phospholipid fatty acids (PLFAs) and terminal restriction fragment length polymorphisms (T-RFLPs) of PCR-amplified 16S ribosomal DNA showed that HM treatment affected the structure of bacterial communities during the 4-year experimental period. Very likely, this is due to the still large bioavailable HM contents in the HM contaminated topsoils at the end of the experiment.     

Fire severity shapes plant colonization effects on bacterial community structure,microbial biomass,and soil enzyme activity in secondary succession of a burned forest

The increasing frequency and severity of wildfires has led to growing attention to the effects of fire disturbance on soil microbial communities and biogeochemical cycling. While many studies have examined fire impacts on plant communities, and a growing body of research is detailing the effects of fire on soil microbial communities, little attention has been paid to the interaction between plant recolonization and shifts in soil properties and microbial community structure and function. In this study, we examined the effect of a common post-fire colonizer plant species, Corydalis aurea, on soil chemistry, microbial biomass, soil enzyme activity and bacterial community structure one year after a major forest wildfire in Colorado, USA, in severely burned and lightly burned soils. Consistent with past research, we find significant differences in soil edaphic and biotic properties between severe and light burn soils. Further, our work suggests an important interaction between fire severity and plant effects by demonstrating that the recolonization of soils by C. aurea plants only has a significant effect on soil bacterial communities and biogeochemistry in severely burned soils, resulting in increases in percent nitrogen, extractable organic carbon, microbial biomass, β-glucosidase enzyme activity and shifts in bacterial community diversity. This work propounds the important role of plant colonization in succession by demonstrating a clear connection between plant colonization and bacterial community structure as well as the cycling of carbon in a post-fire landscape. This study conveys how the strength of plant–microbe interactions in secondary succession may shift based on an abiotic context, where plant effects are accentuated in harsher abiotic conditions of severe burn soils, with implications for bacterial community structure and enzyme activity.     

Physiological and DNA fingerprinting of the bacterial community of Meloidogyne fallax egg masses

Bacterial communities associated with the plant-parasitic nematode Meloidogyne fallax egg masses were compared with those present in the rhizoplane. Two agricultural soils with different nematode population dynamics were used in a glasshouse study, with either potato or tomato as host plant for the nematode. DNA fingerprints and bacterial community level physiological profiles (CLPP) were studied using PCR-DGGE of 16S rRNA genes and Biolog Eco MicroPlates. CLPP and DNA fingerprinting both showed differences between egg mass and rhizoplane bacterial communities. PCR-DGGE showed some bands specific to the egg mass samples. These bands were present in egg masses from both soils. This study shows that egg masses of M. fallax have a distinct bacterial community from that of the adjacent rhizoplane. Soil and host plant factors interactively influence the bacterial egg mass community. Differences in nematode population dynamics between the sample sites cannot be clearly related to the observed differences in the egg mass microbial communities.     

Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO₂ Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO₂ did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.     

Leaf litter is the main driver for changes in bacterial community structures in the rhizosphere of ash and beech

The rhizosphere and the surrounding soil harbor an enormous microbial diversity and a specific community structure, generated by the interaction between plant roots and soil bacteria. The aim of this study was to address the influences of tree species, tree species diversity and leaf litter on soil bacterial diversity and community composition. Therefore, mesocosm experiments using beech, ash, lime, maple and hornbeam were established in 2006, and sampled in October 2008 and June 2009. Mesocosms were planted with one, three or five different tree species and treated with or without litter overlay.Cluster analysis of DGGE-derived patterns revealed a clustering of 2008 sampled litter treatments in two separated clusters. The corresponding treatments sampled in 2009 showed separation in one cluster. PCA analysis based on the relative abundance of active proteobacterial classes and other phyla in beech and ash single-tree species mesocosm indicated an effect of sampling time and leaf litter on active bacterial community composition. The abundance of next-generation sequencing-derived sequences assigned to the Betaproteobacteria was higher in the litter treatments, indicating a higher activity, under these conditions. The Deltaproteobacteria, Nitrospira and Gemmatimonadetes showed an opposite trend and were more active in the mesocosms without litter. The abundance of alphaproteobacterial sequences was higher in mesocosms sampled in 2009 (P = 0.014), whereas the Acidobacteria were more active in 2008 (P = 0.014). At the family level, we found significant differences of the litter vs. non-litter treated group. Additionally, an impact of beech and ash as tree species on soil bacterial diversity was confirmed by the Shannon and Simpson indices. Our results suggest that leaf litter decomposition in pH-stable soils affect the soil bacterial composition, while tree species influence the soil bacterial diversity.     

A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction

We designed an oligonucleotide microarray using probe sequences based upon a phylogenetic analysis of 16S rRNA genes recovered from members of the bacterial division Acidobacteria. A total of 42,194 oligonucleotide probes targeting members of the Acidobacteria division at multiple phylogenetic levels were included on a high-density microarray. Positive control hybridizations revealed a linear relationship between hybridization signal and template concentration, and a substantial decrease in non-specific hybridization was achieved through the addition of 2.5 M betaine to the hybridization buffer. A mean hybridization signal value was calculated for each Acidobacteria lineage, with the resultant lineage-specific hybridization data revealing strong predictive value for the positive control hybridizations. The Acidobacteria phylochip was then used to evaluate Acidobacteria rRNA genes from a Wisconsin soil and within a soil clay fraction. The Acidobacteria hybridization profile revealed the predominance of Acidobacteria subdivisions four and six, and also suggested a decrease in the abundance of subdivision six relative to subdivision four in the soil clay fraction. The change in relative abundance of these subdivisions in a soil clay fraction was supported by data from quantitative PCR. These results support the utility of a phylogenetic microarray in revealing changes in microbial population-level distributions in a complex soil microbial assemblage.     

Rapid changes in the rhizosphere bacterial community structure during re-colonization of sterilized soil

Diversity has been shown to be pivotal in ecosystem stability and resilience. It is therefore important to increase our knowledge about the development of diversity. The aim of this study was to investigate the temporal dynamics of the bacterial community structure in the rhizosphere of wheat plants growing in a soil in which the initial conditions for bacterial re-colonization were modified by mixing different amounts of sterilized with native soil at ratios of 19:1, 9:1, 4:1 and 1:1. Additional treatments comprised sterilized soil or native soil. Plant dry weight at day 20 decreased with increasing percentage of native soil in the mix. The bacterial community structure in the rhizosphere was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) at days 3, 14 and 20 after planting. The bacterial community in the sterilized soil had a lower diversity and evenness than the native soil. Both diversity and evenness increased with time in the sterilized soil. Community structure in the different mixes changed over time and the changes were mix-specific. Principal component analyses of the DGGE banding patterns showed clear differences between the treatments particularly at day 3 and day 14 and revealed changes in community structure within a few days in a given treatment. The results of the present study show that bacterial communities rapidly re-colonize sterilized soil. During re-colonization, the community structure changes rapidly with a general trend towards higher diversity and evenness. The changes in community structure over time are also affected by the amount of sterile substrate to be re-colonized.     

Application of DGGE analysis to the study of bacterial community structure in plant roots and in nonrhizosphere soil

To analyze the structure of bacterial communities in spinach roots and in the nonrhizosphere soil, we used PeR-amplified 16S rRNA gene fragments separated by denaturing gradient gel electrophoresis (DGGE). DGGE revealed a large number of band patterns, which were ascribed to various bacterial species composing each of the bacterial communities. The pattern from the roots was less complex than that from the soil. It is considered that DGGE analysis is suitable for studies of bacterial community structure in soil-plant ecosystems.     

Bacterial community structure of nirK-bearing denitrifiers and the development of properties of soils in created mitigation wetlands

We investigated the abundance and genetic heterogeneity of bacterial nitrite reductase genes (nir) and soil structural properties in created and natural freshwater wetlands in the Virginia piedmont. Soil attributes included soil organic matter (SOM), total organic carbon (TOC), total nitrogen (TN), pH, gravimetric soil moisture (GSM), and bulk density (D_b). A subset of soil attributes were analyzed across the sites, using euclidean cluster analysis, resulting in three soil condition (SC) groups of increasing wetland soil development (i.e., SC1 < SC2 < SC3; less to more developed or matured) as measured by accumulation of TOC, TN, the increase of GSM, and the decrease of D_b. There were no difference found in the bacterial community diversity between the groups (p = 0.4). NirK gene copies detected ranged between 3.6 × 10⁴ and 3.4 × 10⁷ copies g⁻¹ soil and were significantly higher in the most developed soil group, SC3, than in the least developed soil group, SC1. However, the gene copies were lowest in SC2 that had a significantly higher soil pH (~6.6) than the other two SC groups (~5.3). The same pattern was found in denitrifying enzyme activity (DEA) on a companion study where DEA was found negatively correlated with soil pH. Gene fragments were amplified and products were screened by terminal restriction fragment length polymorphism (T-RFLP) analysis. Among 146 different T-RFs identified, fourteen were dominant and together made up more than 65% of all detected fragments. While SC groups did not relate to whole nirK communities, most soil properties that identified SC groups did significantly correlate to dominant members of the community.     

The influence of soil properties on the structure of bacterial and fungal communities across land-use types

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.     

Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Little is known about the organisms responsible for decomposition in terrestrial ecosystems, or how variations in their relative abundance may influence soil carbon (C) cycling. Here, we altered organic matter in situ by manipulating both litter and throughfall inputs to tropical rain forest soils, and then used qPCR and error-corrected bar-coded pyrosequencing to investigate how the resulting changes in soil chemical properties affected microbial community structure. The plot-scale manipulations drove significant changes in microbial community composition: Acidobacteria were present in greater relative abundance in litter removal plots than in double-litter plots, while Alphaproteobacteria were found in higher relative abundance in double-litter and throughfall reduction plots than in control or litter removal plots. In addition, the bacterial:archaeal ratio was higher in double-litter than no-litter plots. The relative abundances of Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were positively correlated with microbial biomass C and nitrogen (N), and soil N and C pools, while acidobacterial relative abundance was negatively correlated with these same factors. Bacterial:archaeal ratios were positively correlated with soil moisture, total soil C and N, extractable ammonium pools, and soil C:N ratios. Additionally, bacterial:archaeal ratios were positively related to the relative abundance of Actinobacteria, Gammaproteobacteria, and Actinobacteria, and negatively correlated to the relative abundance of Nitrospira and Acidobacteria. Together, our results support the copiotrophic/oligotrophic model of soil heterotrophic microbes suggested by Fierer et al. (2007).     

Additions of maize root mucilage to soil changed the structure of the bacterial community

The organic compounds released from roots (rhizodeposits) stimulate the growth of the rhizosphere microbial community. They may be responsible for the differences in the structure of the microbial communities commonly observed between the rhizosphere and the bulk soil. Rhizodeposits consists of a broad range of compounds including root mucilage. The aim of this study was to investigate if additions of maize root mucilage, at a rate of 70 μg C g⁻¹ day⁻¹ for 15 days, to an agricultural soil could affect the structure of the bacterial community. Mucilage additions moderately increased microbial C (+23% increase relative to control), which suggests that the turnover rate of microorganisms consuming this substrate was high. Consistent with this, the number of cultivable bacteria was enhanced by +450%. Catabolic (Biolog^® GN2) and 16S-23S intergenic spacer fingerprints exhibited significant differences between control and mucilage treatments. These data indicate that mucilage can affect both the metabolic and genetic structure of the bacterial community as shown by a greater catabolic potential for carbohydrates. We concluded that mucilage is likely to significantly contribute to differences in the structure of the bacterial communities present in the rhizosphere compared to the bulk soil.