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).     

Analysis of the microbial communities in soils of different ages following volcanic eruptions

Volcanism is a primary process of land formation.It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments.The objective of this study was to identify the microbial communities involved in soil formation.DNA was extracted from soil samples from the Llaima volcano in Chile at sites destroyed by lava in different centuries(1640,1751,and 1957).Bacterial and archaeal 16 S r RNA genes were analyzed using quantitative polymerase chain reaction(q PCR)and Illumina Mi Seq sequencing.Results showed that microbial diversity increased with soil age,particularly between the 1751 and 1640 soils.For archaeal communities,Thaumarchaeota was detected in similar abundances in all soils,but Euryarchaeota was rare in the older soils.The analysis of bacterial 16 S r RNA genes showed high abundances of Chloroflexi(37%),Planctomycetes(18%),and Verrucomicrobia(10%)in the youngest soil.Proteobacteria and Acidobacteria were highly abundant in the older soils(16%in 1640 and 15%in 1751 for Acidobacteria;38%in 1640 and 27%in 1751 for Proteobacteria).The microbial profiles in the youngest soils were unusual,with a high abundance of bacteria belonging to the order Ktedonobacterales(Chloroflexi)in the 1957 soil(37%)compared with the 1751(18%)and 1640(7%)soils.In this study,we show that there is a gradual establishment of the microbial community in volcanic soils following an eruption and that specific microbial groups can colonize during the early stages of recovery.     

Comparisons of different hypervariable regions of rrs genes for fingerprinting of microbial communities in paddy soils

The use of molecular approaches based on 16S rDNA-PCR in microbial ecology has revealed a tremendous prokaryotic diversity in environmental samples. However, there is little or no systematic evaluation of the impacts of hypervariable (V) regions of rrs genes choice on microbial community analysis in soil samples, especially the detailed information about the dominant groups preferentially amplified by different primer pairs. In the present study, eight primer pairs were detected to compare the different V regions for fingerprinting microbial communities in a paddy soil irrigated with petroleum-wastewater, using denaturing gradient gel electrophoresis (DGGE) and amplified ribosomal DNA restriction analysis (ARDRA) techniques. Results reveal the obvious PCR bias produced by different V regions. Both ARDRA analysis of 16S rDNA clone library and DGGE suggest that V₁-V₃ region amplified with primer pair 8f-519r produced the most informative fingerprinting profiles. Additionally, V₃-V₅ region amplified with 341f-907r was another preferable choice for microbial diversity in petroleum-contaminated soil. The V₄-V₅ region and single V region (V₁, V₃, and V₈) were not recommended for the future study of microbial diversity in soil samples. Phylogenetic analysis of 123 sequences from libraries constructed by amplicons generated from six different V regions suggests that different dominant groups were amplified with distinct primer sets. In detail, V₁-V₃ library (amplified with 8f-519r) and V₃-V₅ library were dominated by Actinobacteria (20.4%) (particularly in genus Arthrobacter), V₁-V₃ library (amplified with 63f-518r) was dominated by γ-Proteobacteria (25.0%) and α-Proteobacteria (22.0%) (particularly in genus Brevundimonas), V₃ library was dominated by β-Proteobacteria (22.3%) (particularly in genus Gallionella) and α-Proteobacteria (20.0%), V₆-V₈ library was dominated by Chlamydiae (20.4%) and β-Proteobacteria (20.4%), V₈ library was dominated by γ-Proteobacteria (27.2%) (particularly in genus Acinetobacter) and β-Proteobacteria (14.0%). The present work strongly recommends that primer pairs should be chosen cautiously in community diversity analysis based on PCR amplification of 16S rDNA, and involving at least two different 16S rDNA universal primer pairs would perform better.     

The relationships among microbial parameters and the rate of organic matter mineralization in forest soils,as influenced by forest type

Vegetation type influences the rate of accumulation and mineralization of organic matter in forest soil, mainly through its effect on soil microorganisms. We investigated the relationships among forest types and microbial biomass C (MBC), basal respiration (R_B), substrate-induced respiration (R_S), N mineralization (N_min), specific growth rate μ, microbial eco-physiology and activities of seven hydrolytic enzymes, in samples taken from 25 stands on acidic soils and one stand on limestone, covering typical types of coniferous and deciduous forests in Central Europe. Soils under deciduous trees were less acidic than soils of coniferous forests, which led to increased mineralizing activities R_B and N_min, and a higher proportion of active microbial biomass (R_S/MBC) in the Of horizon. This resulted in more extractable organic C (0.5 M K₂SO₄) in soils of deciduous forests and a higher accumulation of soil organic matter (SOM) in coniferous forest soil. No effect of forest type on the microbial properties was detected in the Oh horizon and in the 0–10 cm layer. The microbial quotient (MBC/C_org), reflecting the quality of organic matter used for microbial growth, was higher in deciduous forests in all three layers. The metabolic quotient qCO₂ (R_B/MBC) and the specific growth rate μ, estimated using respiration growth curves, did not differ in soils of both forest types. Our results showed that the quality of SOM in coniferous forests supported microorganisms with higher activities of β-glucosidase, cellobiosidase and β-xylosidase, which suggested the key importance of fungi in these soils. Processes mediated by bacteria were probably more important in deciduous forest soils with higher activities of arylsulphatase and urease. The results from the stand on limestone showed that pH had a positive effect on microbial biomass and SOM mineralization.     

长期施肥对黑土农田土壤微生物群落的影响

基于中国科学院海伦农业生态试验站长期定位试验区,应用实时荧光定量PCR(Real-time PCR)和变性梯度凝胶电泳(DGGE)技术研究了无施肥(NF)、单施N、P化肥(NP)以及化肥配施有机猪粪肥(NPM)等3种长期施肥措施对黑土区玉米田土壤微生物群落密度和结构的影响.Real-time PCR方法定量NF、NP及NPM措施土壤细菌群落基因组DNA质量分别为381、1 351和1 773 ng g-1干土,真菌群落基因组DNA质量分别113.3、127.3和20.6 ng g-1干土,真菌与细菌的比率分别为0.31、0.09和0.01,NPM措施显著低于另两种施肥方式(p＜0.05).DGGE方法研究表明,NP和NPM措施不能改善土壤细菌和真菌群落的多样性、均匀性及优势菌优势程度;但主成分分析结果显示NP和NPM措施均可改变土壤细菌和真菌群落的构成,且真菌群落的变化更为显著;聚类分析结果显示NP和NPM措施下细菌群落结构较相近,其相似系数为0.89,真菌群落中NP措施与NF措施相近,相似系数为0.63,高于NP与NPM措施的相似系数0.51.上述结果表明有机猪粪肥的长期施用可以显著降低黑土农田土壤真菌与细菌的比率,且明显地改变土壤细菌和真菌群落的结构.     

模拟干湿交替对水稻土古菌群落结构的影响

干湿交替是自然界普遍存在的现象,但长期以来由于技术的限制,复杂土壤中微生物对水分变化的响应规律仍不清楚。针对我国江苏常熟湖泊底泥发育的典型水稻土,在室内开展湿润-风干以及风干-湿润各三次循环,每次循环中湿润、风干状态各维持7d,利用微生物核糖体rRNA的通用引物进行PCR扩增,通过高通量测序分析土壤古菌多样性变化,同时结合实时荧光定量PCR技术,在DNA和RNA水平研究古菌数量对干湿交替过程的响应规律。结果表明:水稻土湿润-风干过程中,在DNA水平土壤古菌数量降幅约为149倍~468倍,而在RNA水平降幅最高仅为2.06倍;水稻土风干-湿润过程中,在DNA水平古菌数量增幅在147倍~360倍之间,而在RNA水平增幅最高仅为2.95倍。表明在干湿交替过程中,DNA水平的古菌16S rRNA基因数量变化远高于RNA水平。基于高通量测序多样性的结果表明,在DNA和RNA水平,湿润土壤3次风干、以及风干土壤3次加水湿润7d恢复后,土壤古菌群落结构均发生统计显著性改变。在微生物门、纲、目、科和属的不同分类水平下,水稻土古菌主要包括3、10、13、14、10种不同的类群,在RNA和DNA水平的结果基本一致。干湿交替导致部分古菌类群发生显著变化,其中在微生物分类学目水平发生显著变化的古菌最高达到6种,主要包括产甲烷古菌和氨氧化古菌,如Methanobacteriales、Methanosarcinales、Methanomicrobiales和Nitrososphaerales等。这些研究结果表明,反复的干湿交替并未显著改变水稻土中古菌的主要类群组成,古菌类群的绝对数量和相对丰度发生了一定程度的变化,但这些变化与微生物生理作用的联系仍需进一步研究;风干土壤中古菌RNA序列极可能来自于完整的古菌细胞,暗示了这些古菌细胞能够较好地适应水稻土中水分的剧烈变化,风干状态的土壤在一定程度也可用于土壤古菌群落组成研究。     

Impact of urine and the application of the nitrification inhibitor DCD on microbial communities in dairy-grazed pasture soils

Tools to manage the emission of the greenhouse gas nitrous oxide (N₂O), an intermediate of both nitrification and denitrification, from soils are limited. To date, the nitrification inhibitor dicyandiamide (DCD) is one of the most effective tools available to livestock farmers for reducing N₂O emissions and minimizing leaching of nitrogen in response to increased urine deposition in grazed pasture systems. Despite its effectiveness in decreasing N losses from animal urine by inhibiting N processes in soils, the effect of DCD on the population structure of denitrifiers and overall bacterial community composition is still uncertain. Here we use three New Zealand dairy-grazed pasture soils to determine the effects of DCD application on microbial community richness and composition at both functional (genes involved in the denitrification process) and phylogenetic (overall bacterial community composition based on 16S rRNA profiling) levels. Results further confirm that the effects on microbial populations are minimal and transient in nature. The impact of DCD on microbial community structure was soil dependent, and a greater effect was attributed to intrinsic soil properties like soil texture, with community response to DCD in combination with urine being comparable to that under urine alone. Addition of DCD to cattle urine also reduced N₂O emission between 23 and 67%.     

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.     

Inputs of nitrogen and organic matter govern the composition of fungal communities in soil disturbed by overwintering cattle

Overwintering cattle outdoors causes soil surface disturbance, substantial increases of soil N_tot, C_org, and P and a shift in pH to alkaline levels. Since fungi predominate in unfertilized soils with acidic pH and have filamentous hyphae, we hypothesized that changes caused by overwintering cattle outdoors (trampling, excreta returns, and changes in soil chemistry) will lead to suppressed species richness, lower biomass, and alter the structure of fungal communities. The research was conducted on an upland pasture used more than 10 years for cattle overwintering. Both culture-dependent and -independent methods were used for the determination of either fungal species composition (cultivation; DGGE) or biomass (numbers of CFU; concentration of fungal PLFA marker 18:2ω6,9). Soils under three different levels of cattle disturbance (S - severe, M - moderate, C - no disturbance/control) were investigated during three subsequent years. In addition, the DGGE analysis of soils was completed by comparison with analysis of fresh cattle excrements (Ex). The composition of fungal communities showed significantly higher richness and a substantial shift in species composition in cattle-disturbed soils (S, M) in comparison to the non-disturbed soil (C). The number of separated DGGE bands was significantly higher in S (30.67 ± 1.63; mean ± SD) and M (25.50 ± 1.64) soils than in the C soil (19.33 ± 1.75). Sequencing of typical bands revealed common fungal genera - Alternaria, Penicillium, Fusarium, Rhizopus, Isaria, and Metarhizium. Profiles of the S soil were enriched by bands of rumen-born anaerobic fungi (Neocallimastix, Cyllamyces) occurring mainly in profiles of excrements, where relatively low band richness (14.33 ± 1.15) was observed. The increasing level of cattle disturbance induced an increase in the biomass of complex fungal community over the three-year experimental period from 3.39 ± 2.11 (mean ± SD) nmol of fungal PLFA per gram of the C soil to 5.87 ± 3.16 in the M soil and 9.21 ± 4.69 in the S soil. Concentrations of soil N_tot and C_org were evaluated as the parameters significantly correlating with biomass as well as composition of the fungal community.     

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.     

Contribution of primary organic matter to the fatty acid pool in agricultural soils

Fatty acids as major compounds of soil lipids may affect many soil properties, but the input and turnover rates in soil are largely unknown. The objective of this study was to identify and quantify fatty acids in soils as a result of input from primary sources such as plant residues, farmyard manure and soil organisms, and to evaluate the corresponding turnover- and stabilization processes. The concentrations of n-C_10:0 to n-C_34:0 fatty acids were determined in the Ap horizon of a Phaeozem with long-term cropping of rye and maize and the treatments ‘Unfertilized’ (‘U’) and fertilized with ‘Farmyard manure’ (‘FYM’). The most important primary sources of fatty acids such as rye and maize stubble and roots, soil micro- and mesofauna, and the applied FYM were also investigated. The quantification of fatty acids by gas chromatography/mass spectrometry (GC/MS) showed that long-term FYM application led to larger concentrations of n-alkyl fatty acids in the plots grown with rye (‘U’: 48.1 μg g⁻¹, ‘FYM’: 57.7 μg g⁻¹, **P≤0.01, n=3) and maize (‘U’: 17.0 μg g⁻¹, ‘FYM’: 23.4 μg g⁻¹, ***P≤0.001, n=3). The observed bimodal fatty acid distribution in soils from n-C_10:0 to n-C_21:0 and from n-C_21:0 to n-C_34:0 with a predominance at n-C_16:0 and at n-C_28:0 was apparently due to input from crop residues, soil organisms and FYM. The short-chain lengths may have originated from the investigated primary sources. The major contributors to the long-chain lengths, with a maximum at n-C_28:0, were rye stubble and FYM. A change in mono-culture from rye to maize, 38 years prior to sampling, led to a decrease in fatty acid concentrations by factors of about 2.8 (‘U’) and 2.5 (‘FYM’). Therefore, rye-derived fatty acids and soil tillage had a larger impact on fatty acid pools than the input of primary organic matter. The changes in fatty acid distributions and pools under the consideration of the quantified input of primary organic matter led to the conclusion that the short-chained fatty acids were more rapidly decomposed than the long-chains.     

Biogeography and biophysicochemical traits link N2O emissions,N2O emission potential and microbial communities across New Zealand pasture soils

The process of denitrification has been studied for decades, with current evidence suggesting that an ecosystem's ability to produce and emit N₂O is controlled both by transient ‘proximal’ regulators (e.g. temperature, moisture, N availability) as well as distal regulators (e.g. soil type, microbial functional diversity, geography). In this study we use New Zealand soils as a model system to test the impact of distal regulators (i.e. geography) on microbial communities and their N₂O emission potential. Using gas chromatography, soil chemical analyses, 16S amplicon sequencing, terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) on three denitrifier functional genes (nirS, nirK and nosZ), we assessed the factors linked to N₂O emissions across a latitudinal gradient. Results show that soil drainage class, soil texture class, and latitude were powerful regulators of both emissions and emission end products (N₂ vs. N₂O). Mixed models demonstrate that a few variables (including latitude, texture class, drainage class and denitrifier community data [abundance and diversity] amongst others) were enough to predict both the amount and type of gas emitted. In addition we show that microbial community composition (based on 16S rRNA gene sequencing) can also be used to predict both the gas species and quantity emitted.     

Thirteen years of continued application of composted organic wastes in a vineyard modify soil quality characteristics

A solution for environmentally wiser agriculture is the use of composted organic wastes as soil amendments. Just as this alleviates the problem of recycling organic residues, it provides necessary nutrient input for food production. The objective of this work was to study the effect that 13 years of applying three different composted organic wastes or organic amendments have had on soil quality, GHG emissions and the dynamics of its microbial communities 15 days after the annual application. For this purpose, in 1996 a field trial was set up in a Tempranillo vineyard. Since 1998, the applied organic amendments have been as follows: 1. a pelletized organic compost (PEL) made from plant, animal and sewage sludge residues; 2. a compost made from the organic fraction of municipal solid waste (OF-MSW); 3. a compost made of stabilized sheep manure (SMC); 4. a mineral fertilizer (NPK); and 5. an unaltered control. The mean annual doses applied since 1998 have been 3700 kg ha⁻¹ fresh weight (FW) of PEL, 4075 kg ha⁻¹ FW of OF-MSW, 4630 kg ha⁻¹ FW of SMC, and 340 kg ha⁻¹ of NPK treatment. Soil quality was consistently enhanced by amendment application over the 13 years. Total nitrogen was significantly increased in PEL (0.1%), OF-MSW (0.09%) and SMC (0.1%) compared to control (0.06%). Nutrient content was also improved in a similar way, e.g. the most significant increase in P Olsen (80.7 mg kg⁻¹) and K₂O (473.8 mg kg⁻¹) was found on SMC. The overall enzyme activity was also increased 15 days after the annual application and OF-MSW had the highest rate (95.9) compared to control (51.3). This increase in metabolic activity was also recorded in GHG emissions. CO₂ equivalents per hectare were 1745 kg for OF-MSW and it was the only significant difference found. PEL with 1598 kg and SMC with 1591 kg were not different from the Control (1104 kg). Even though GHG emissions in the soil increased because of the application, soil organic matter content increased significantly (at least 35% more in all organic treatments compared to control) and this rise in organic matter was consistent over the years. According to the results, 85% of the sequences corresponded to 5 main phyla: Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria and Gemmatimonadetes, with unclassified material making up for 10.9% (average) of the sequences. Bacterial diversity by Shannon and Chao1 indices was not affected 15 days after the application. However, slight changes in the bacterial community were recorded 15 days after application only in OF-MSW treatment. Assessing soil quality using these three factors allows the relevant agronomical capabilities of the soil to be integrated with the potential effect of this practise on global warming.     

Soil microbial biomass and organic matter composition in soils under cultivation

To determine whether there is a relationship between the composition of soil organic matter and the activity of the soil microbial biomass, the composition of the organic matter in 12 typical arable soils in Northwest Germany was investigated by wet chemical analysis and CPMAS cross polarization magic angle spinning ¹³C-NMR spectroscopy. The data were correlated with the microbial biomass as estimated by substrate-induced respiration. A strong correlation between the microbial biomass and alkylic C compounds was observed (r=-0.960^***). Recalcitrant substances were enriched in this fraction, which were classified as humic acids according to the wet chemical procedure. The microbial decomposition of these humic acids is probably retarded, due to their chemical structure and/or physical bonding, when the soil microbial biomass activity is limited.     

Mineralization rate of C-labelled dissolved organic matter from leaf litter in soils of a weathering chronosequence

During the processes of primary succession and soil development, large stocks of organic C with very long residence times accumulate in many soils. Soluble organic C adsorbed by soils may contribute to the stock of organic C accumulating during soil development. We determined whether the mineralization rate of water-soluble organic C and the insoluble residue from ¹⁴C-labelled leaf litter added to soils from a weathering chronosequence decrease as soil age and adsorption capacity increase. The soils were formed on mudflows of andesitic material deposited about 75, 255, 616 y ago, and another older but undetermined time before this study. The percentage of the DOC adsorbed by the soils increased with age. After 1 year of incubation there were no significant differences in the mineralization rates of DOC added to soils of different ages. The DOC appeared to be comprised of two fractions, one that comprises about 32% of the total that mineralized with a half decay time of 0.02 y (7 d) and a second fraction comprising 68% with a half decay time of about 1.6 y. Consequently, the slowly mineralized fraction of the soluble C contributed to the accumulation of slowly mineralized C in the soil. Both the slowly and rapidly mineralized fractions of the insoluble residue decomposed more slowly than the corresponding fractions in DOC. We found no support for the idea that increased adsorption capacity due to weathering resulted in protection of soluble organic C from microbial mineralization.     

Biochemical properties and biodegradation of dissolved organic matter from soils

Various biologically mediated processes are involved in the turnover of dissolved organic matter (DOM) in soil; however, relatively little is known about the dynamics of either the microbial community or the individual classes of organic molecules during the decomposition of DOM. We examined the net loss of DOC, the mineralisation of C to CO₂ and the degradation of DOC from six different soils by soil microorganisms. We also quantified the changes in the concentrations of protein, carbohydrate and amino acid C during microbial biodegradation. Over a 70-day incubation period at 20°C, the mineralisation of DOC to CO₂ was described by a double exponential model with a labile pool (half-life, 3–8 days) and a stable pool (half-life, 0.4–6 years). However, in nearly all cases, the mass loss of DOC exceeded the C released as CO₂ with significant deviations from the double exponential model. Comparison of mass DOC loss, CO₂ production and microbial cell counts, determined by epifluorescence microscopy, showed that a proportion of the lost DOC mass could be accounted for by microbial assimilation. Carbohydrate and protein C concentrations fluctuated throughout the incubation with a net change of between 3 to 13 and −30 to 22.4% initial DOC, respectively. No amino acid C was detected during the incubation period (level of detection, 0.01 mg C l⁻¹).     

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.