Effects of inorganic fertilizer and manure on soil archaeal abundance at two experimental farms during three consecutive rotation-cropping seasons

Soil archaeal population dynamics at two experimental sites of the same clay-loam type in Ottawa and Woodslee, Ontario, were investigated to determine fertilizer and manure effects following their different long-term crop rotation and fertilization schemes. Phylogenetic analysis of cloned soil archaeal 16S rRNA gene libraries of both sites identified them with group 1.1b of Thaumarchaeota. The gene population dynamics subtly varied in the order of 10⁷ copies g⁻¹ soil when monitored by quantitative real-time PCR during three growing seasons (2007–2009). In Ottawa, where plots were amended with dairy-farm manure, soil thaumarchaeal gene abundance was double of the unamended plots. At the Woodslee N-P-K-fertilized plots, it remained at least 30% fewer than that of the unfertilized ones. These cultivated plots showed soil carbon limitation while the fertilized ones were low in soil pH (ca. 5.5). Surface soils from an unfertilized sod plot and an adjacent deciduous forest had higher total carbon content (C:N ratio of 9 and 11, respectively). Their thaumarchaeal gene abundance varied up to 4.8 × 10⁷ and 7.0 × 10⁷ copies g⁻¹ soil, respectively. The former value was also attained at the manure-amended plots in Ottawa, where the C:N ratio was just below 10. Where soil pH was above 6.0, there was a weak and positive correlation between soil total C and the estimated gene abundance. Such gene population dynamics consistently demonstrated the stimulating and suppressive effects of dairy-farm manure (Ottawa site) and inorganic fertilizers (Woodslee site), respectively, on soil thaumarchaea. At both sites archaeal amoA and 16S rRNA gene abundance were similarly affected. Archaeal amoA gene abundance also outnumbered bacterial amoA abundance, suggesting that ammonia-oxidizing archaea might be dominant in these soils. Only minor crop effects on gene population dynamics were detected.     

Microbial Community Changes Along a Land-Use Gradient of Desert Soil Origin

Soil harbors remarkably stabilize bacterial communities at the phylum level.However,no two soils have exactly the same structure of bacterial phyla.The structure of microbial community is strongly influenced by the type of land-use through changes in soil attributes.Using high-throughput pyrosequencing and quantitative polymerase chain reaction techniques,soil microbial community structures were investigated along a land-use gradient of 100- and 27-year farmlands,a 33-year Pinus forest,a 28-year poplar forest,and a 21-year shrubland,as well as a native desert from which all cultivated systems were converted.The results revealed that the dominant phylotypes in the native soil comprised primarily of Alphaproteobacteria,Actinobacteria,Bacteroidetes,and Firmicutes,accounting for >71.4%of the total bacterial 16S rRNA sequence reads.Changes in land-use led to a significant decrease in these dominant phylotypes down to 33.4%.In contrast,the phylotypes with low abundance,such as Acidobacteria,Chloroflexi,Nitrospira,and Gammaproteobacteria,increased sharply from 4.5%-5.9%in the native soil to 20.9%-30.2%of the total 16S rRNA gene sequences in the cultivated soils except for the soil from the shrubland.These contrasting changes in the major taxa appear to be correlated with the changes in soil attributes.For instance,bacterial and archaeal amoA genes were found to be 960-and 3 800-fold more abundant in the soil from the 100-year farmland than the native soil.The changes in numerically less dominant nitrifying phylotypes are consistent with soil inorganic nitrogen dynamics.Quantification of the 16S rRNA genes demonstrated that bacteria and archaea were about two to three orders of magnitude more abundant in the cultivated soil than in the native soil.Hence,land-use type affects the soil bacterial community structure,which has profound consequences on ecosystem function.     

Activity and composition of the methanogenic archaeal community in soil vegetated with wild versus cultivated rice

Wild rice (Oryza rufipogon) is a problematic weed in fields of cultivated rice (Oryza sativa). We hypothesized that the composition and/or the activity of the methanogenic microbial communities might be different in soil grown with cultivated versus wild rice. We used samples from Hainan, China, where wild rice grew on a field adjacent to cultivated rice. The composition of the methanogenic archaeal community was analyzed in samples of rice soil by targeting the 16S rRNA gene. Analysis of the terminal restriction fragment length polymorphism (T-RFLP) showed similar patterns in soil from wild versus cultivated rice. Sequences of archaeal 16S rRNA genes also showed similar composition in soil from wild versus cultivated rice, revealing the presence of Methanosarcinaceae, Methanosaetaceae, Methanobacteriales, Methanocellales (Rice Cluster I), Rice Cluster II, Crenarchaeota Group I.3 and Crenarchaeota Group I.1b. Incubation of soil samples under anoxic conditions generally resulted in vigorous CH₄ production after a lag phase of 7-8 days. Production of CH₄ was partially inhibited by methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, resulting in nearly stoichiometric accumulation of acetate. CO₂ was produced without lag phase. The δ¹³C of the produced CO₂ was slightly lower in soil grown with cultivated rice versus wild rice, reflecting the δ¹³C of organic matter, which was about −29‰ for cultivated rice soil and about −24‰ for wild rice soil. The δ¹³C of the produced CH₄ and the acetate that accumulated in the presence of CH₃F was much more negative in cultivated versus wild rice soil, mainly since the isotopic fractionation factors for hydrogenotrophic methanogenesis were higher for soil from cultivated rice (α = 1.054) versus wild rice (α = 1.039). However, the percentage contribution of hydrogenotrophic methanogenesis to total CH₄ production was similar in both soils (27-35%). In conclusion, although the two soils exhibited different δ¹³C values of soil organic matter and derived products, they were similar with respect to rates and composition of the methanogenic communities.     

油井采出液中微生物群落结构的T-RFLP分析

应用末端标记限制性片段长度多态性(Terminal Restriction Fragment Length Polymorphism,T-RFLP)和克隆文库分析,以微生物群落16SrRNA基因(16S rDNA)为目标,对大庆油田过渡带油井采出液(于2005年7月和10月取样)中的微生物群落结构进行了解析和比较。T-RFLP分析表明,2005年7月和10月油井采出液中古菌群落结构较为单一,随时间变化不大;而细菌群落结构较为复杂,不同时间群落中的优势菌有明显的差别。古菌和细菌16S rDNA片段测序和系统发育分析表明,大庆油田过渡带油井采出液古菌群落中的优势菌均为产甲烷菌;细菌群落中的优势菌则与β、γ、δ、ε变形杆菌(Proteobacteria)、拟杆菌(Bacte-roidetes)和脱铁杆菌(Deferribacteres)有较高的相似性,细菌群落中检出了大量的未培养微生物(Deep-branching lineages)。     

Differences in the activity and bacterial community structure of drained grassland and forest peat soils

The microbial activity and bacterial community structure were investigated in two types of peat soil in a temperate marsh. The first, a drained grassland fen soil, has a neutral pH with partially degraded peat in the upper oxic soil horizons (16% soil organic carbon). The second, a bog soil, was sampled in a swampy forest and has a very high soil organic carbon content (45%), a low pH (4.5), and has occasional anoxic conditions in the upper soil horizons due to the high water table level. The microbial activity in the two soils was measured as the basal and substrate-induced respiration (SIR). Unexpectedly, the SIR (μl CO₂ g⁻¹ dry soil) was higher in the bog than in the fen soil, but lower when CO₂ production was expressed per volume of soil. This may be explained by the notable difference in the bulk densities of the two soils. The bacterial communities were assessed by terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA genes and indicated differences between the two soils. The differences were determined by the soil characteristics rather than the season in which the soil was sampled. The 16S rRNA gene libraries, constructed from the two soils, revealed high proportions of sequences assigned to the Acidobacteria phylum. Each library contained a distinct set of phylogenetic subgroups of this important group of bacteria.     

Biochar soil amendment increased bacterial but decreased fungal gene abundance with shifts in community structure in a slightly acid rice paddy from Southwest China

Biochar’s role on greenhouse gas emission and plant growth has been well addressed. However, there have been few studies on changes in soil microbial community and activities with biochar soil amendment (BSA) in croplands. In a field experiment, biochar was amended at rates of 0, 20 and 40 t ha⁻¹ (C0, C1 and C2, respectively) in May 2010 before rice transplantation in a rice paddy from Sichuan, China. Topsoil (0–15 cm) was collected from the rice paddy while rice harvest in late October 2011. Soil physico-chemical properties and microbial biomass carbon (MBC) and nitrogen (MBN) as well as selected soil enzyme activities were determined. Based on 16S rRNA and 18S rRNA gene, bacterial and fungal community structure and abundance were characterized using terminal-restriction fragment length polymorphism (T-RFLP) combined with clone library analysis, denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR assay (qPCR). Contents of SOC and total N and soil pH were increased but bulk density decreased significantly. While no changes in MBC and MBN, gene copy numbers of bacterial 16S rRNA was shown significantly increased by 28% and 64% and that of fungal 18S rRNA significantly decreased by 35% and 46% under BSA at 20 and 40 t ha⁻¹ respectively over control. Moreover, there was a significant decrease by 70% in abundance of Methylophilaceae and of Hydrogenophilaceae with an increase by 45% in Anaerolineae abundance under BSA at 40 t ha⁻¹ over control. Whereas, using sequencing DGGE bands of fungal 18S rRNA gene, some bands affiliated with Ascomycota and Glomeromycota were shown inhibited by BSA at rate of 40 t ha⁻¹. Significant increases in activities of dehydrogenase, alkaline phosphatases while decreased β-glucosidase were also observed under BSA. The results here indicated a shift toward a bacterial dominated microbial community in the rice paddy with BSA.     

Response of ammonia oxidizing microbes to the stresses of arsenic and copper in two acidic alfisols

Soil pollution by elevated heavy metals exhibits adverse effects on soil microorganisms. Ammonia oxidizing bacteria and ammonia oxidizing archaea perform ammonia oxidative processes in acidic soils. However, influence of heavy metal stress on soil ammonia oxidizers distribution and diversity is inadequately addressed. This study investigated the responses of ammonia oxidizing bacteria and archaea to heavy metals, Cu and As during short-term laboratory experiment. Two different acidic alfisols named as Rayka and Hangzhou spiked with different concentrations of As, Cu and As + Cu were incubated for 10 weeks. Significant reduction in copy numbers of archaeal-16S rRNA, bacterial-16S rRNA and functional amoA genes was observed along elevated heavy metal concentrations. Ammonia oxidizing archaea was found to be more abundant than ammonia oxidizing bacteria in all the heavy metal treatments. The potential nitrification rate significantly decreased with increasing As and Cu concentrations in the two soils examined. Denaturing gradient gel electrophoresis analysis revealed no apparent community shift for ammonia oxidizing archaea even at higher concentrations of As and Cu. Phylogenetic analysis of archaeal amoA gene from 4 clone libraries indicated that all the archaeal amoA sequences were placed within 3 distinct clusters from soil and sediment group 1.1b of Thaumarchaeota. Our results could be useful for the better understanding of the ecological effects of heavy metals on the abundance and diversity of soil ammonia oxidizers.     

Bacterial community structure in fumigated soil

Soil microbial biomass has been determined since the mid 1970's by the chloroform fumigation incubation technique as proposed by Jenkinson and Powlson (1976). The microbial biomass C can be determined by subtracting the CO₂ emitted from an unfumigated soil (mineralization of soil organic matter) from that emitted from a chloroform fumigated inoculated soil (mineralization of soil organic matter and killed soil microorganisms) and dividing the difference by a proportionality factor (k_C = 0.45). The question remained which microorganisms recolonized a fumigated soil. An arable soil was fumigated for one day with ethanol-free chloroform or left unfumigated and incubated aerobically after removal of the chloroform for 10 days. The bacterial population structures were determined in the fumigated and unfumigated soil after 0, 1, 5 and 10 days by means of 454 pyrosequencing of the 16S rRNA gene. Fumigating the arable soil reduced significantly the relative abundance of phylotypes belonging to different groups, but increased the relative abundance of only four genera belonging to two phyla (Actinobacteria and Firmicutes) and two orders (Actinomycetales and Bacillales). The relative abundance of phylotypes belonging to the Micromonospora (Micromonosporaceae) increased significantly from 0.2% in the unfumigated soil to 6.7% in the fumigated soil and that of Bacillus (Bacillaceae) from 3.6% to 40.8%, Cohnella (Paenibacillaceae) from undetectable amounts to 0.6% and Paenibacillus (Paenibacillaceae) from 0.3% to 4.2%. The relative percentage of phylotypes belonging to the Acidobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Proteobacteria (α- β-, δ- and γ-Proteobacteria) were significantly lower in the fumigated than in the unfumigated soil and in most of them the relative abundance of different bacterial orders (i.e. Gp3, Gp4, Gp6, Sphingobacteriales, Gemmatimonadales, Rhodospirillales, Burkholderiales, Xanthomonadales) was reduced strongly (P < 0.001). It was found that the relative abundance of a wide range of bacteria was reduced shortly after fumigating an arable soil, but only a limited group of bacteria increased in a fumigated arable soil indicating a capacity to metabolize the killed soil microorganisms or recolonize a fumigated soil.     

Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico

In recent years, there has been a growing need to understand how salinity affects microbial communities in agricultural soils. Archaeal and bacterial community diversities and structures were investigated by high-throughput sequencing analysis of their 16S rRNA in two arable soils with low electrical conductivity(EC)(2.3 and 2.6 dS m^-1) and a saline soil(EC = 17.6 dS m^-1). The dominant bacterial phyla in the soils were Proteobacteria(relative abundance(RA) = 46.2%), followe...     

Effects of municipal solid waste compost,farmyard manure and chemical fertilizers on wheat growth,soil composition and soil bacterial characteristics under Tunisian arid climate

The use of municipal solid waste compost (MSWC) as soil organic amendment is of an economic and environmental interest. However, little is known about the effectiveness of MSWC application on agricultural soil in northern Africa arid climate. We assessed the impact of five years' applications of different organic and mineral fertilizers on wheat grain yields and soil chemical and microbial characteristics. Soils were treated with MSWC at rates of 40 (C1) and 80 (C2) Mg ha^?1, farmyard manure at a rate of 40 Mg ha^?1 (M), chemical fertilizers (Cf) and the combinations (C1Cf, C2Cf, MCf). Wheat grain yield was enhanced with all amendments. Parallel increases of heavy metal levels and faecal coliform were also recorded except for Cf treatments. Based on wheat grain yield, heavy metal and faecal coliform data, we determined the treatment effectiveness index (E_xx), calculated by dividing the pollutant increase ratio by the grain yield increase ratio. The treatment effectiveness index E_C1 indicated lower faecal and heavy metal pollution with positive gains in wheat yields. Despite polluting effects on soil determined by the different treatments, no significant differences between treatments were observed in total bacterial count and soil bacterial community structure, as shown by 16S rRNA gene PCR-denaturing gradient gel electrophoresis banding patterns and 16S rRNA gene Length Heterogeneity-PCR analysis. According to the collected data, the use of MSWC at a rate of 40 Mg ha^?1 might be recommended.     

Methane production potential and methanogenic archaeal community structure in tropical irrigated Indian paddy soils

Soil characteristics regulate various belowground microbial processes including methanogenesis and, consequently, affect the structure and function of methanogenic archaeal communities due to change in soil type which in turn influences the CH₄ production potential of soils. Thus, five different soil orders (Alfisol, Entisol, Inceptisol, Podzol and Vertisol) were studied to assess their CH₄ production potential and also the methanogenic archaeal community structure in dryland irrigated Indian paddy soils. Soil incubation experiments revealed CH₄ production to range from 178.4 to 431.2 μg CH₄ g^-1 dws in all soil orders as: Vertisol<Inceptisol<Entisol<Podzol<Alfisol. The numbers of methanogens as quantified using real-time quantitative polymerase chain reaction (qPCR) targeting mcrA genes varied between 0.06 and 72.97 (×10⁶ copies g^-1 dws) and were the highest in Vertisol soil and the least in Alfisol soil. PCR-denaturing gradient gel electrophoresis (DGGE)-based approach targeting 16S rRNA genes revealed diverse methanogenic archaeal communities across all soils. A total of 43 DGGE bands sequenced showed the closely related groups to Methanomicrobiaceae, Methanobacteriaceae, Methanocellales, Methanosarcinaceae, Methanosaetaceae and Crenarchaeota. The composition of methanogenic groups differed among all soils and only the Methanocellales group was common and dominant in all types of soils. The highest diversity of methanogens was found in Inceptisol and Vertisol soils. Methane production potential varied significantly in different soil orders with a positive relationship (p?<?0.05) with methanogens population size, permanganate oxidizable C (POXC) and CO₂ production. The present study suggested that CH₄ production potential of different soils depends on physicochemical properties, methanogenic archaeal community composition and the population size.     

Impacts of different N management regimes on nitrifier and denitrifier communities and N cycling in soil microenvironments

Real-time quantitative PCR assays, targeting part of the ammonia monooxygenase (amoA), nitrous oxide reductase (nosZ), and 16S rRNA genes were coupled with ¹⁵N pool dilution techniques to investigate the effects of long-term agricultural management practices on potential gross N mineralization and nitrification rates, as well as ammonia-oxidizing bacteria (AOB), denitrifier, and total bacterial community sizes within different soil microenvironments. Three soil microenvironments [coarse particulate organic matter (cPOM; >250 μm), microaggregate (53-250 μm), and silt-and-clay fraction (<53 μm)] were physically isolated from soil samples collected across the cropping season from conventional, low-input, and organic maize-tomato systems (Zea mays L.-Lycopersicum esculentum L.). We hypothesized that (i) the higher N inputs and soil N content of the organic system foster larger AOB and denitrifier communities than in the conventional and low-input systems, (ii) differences in potential gross N mineralization and nitrification rates across the systems correspond with AOB and denitrifier abundances, and (iii) amoA, nosZ, and 16S rRNA gene abundances are higher in the microaggregates than in the cPOM and silt-and-clay microenvironments. Despite 13 years of different soil management and greater soil C and N content in the organic compared to the conventional and low-input systems, total bacterial communities within the whole soil were similar in size across the three systems (∼5.15 × 10⁸ copies g⁻¹ soil). However, amoA gene densities were ∼2 times higher in the organic (1.75 × 10⁸ copies g⁻¹ soil) than the other systems at the start of the season and nosZ gene abundances were ∼2 times greater in the conventional (7.65 × 10⁷ copies g⁻¹ soil) than in the other systems by the end of the season. Because organic management did not consistently lead to larger AOB and denitrifier communities than the other two systems, our first hypothesis was not corroborated. Our second hypothesis was also not corroborated because canonical correspondence analyses revealed that AOB and denitrifier abundances were decoupled from potential gross N mineralization and nitrification rates and from inorganic N concentrations. Our third hypothesis was supported by the overall larger nitrifier, denitrifier, and total bacterial communities measured in the soil microaggregates compared to the cPOM and silt-and-clay. These results suggest that the microaggregates are microenvironments that preferentially stabilize C, and concomitantly promote the growth of nitrifier and denitrifier communities, thereby serving as potential hotspots for N₂O losses.     

不同类型水稻土微生物群落结构特征及其影响因素

选取基于我国土壤地理发生分类的不同类型土壤发育的四种水稻土,利用¹⁵N₂气体示踪法测定生物固氮速率,采用实时荧光定量PCR（Real-time PCR）技术测定细菌丰度,通过16S rRNA基因高通量测序分析微生物群落组成和多样性。结果表明：变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）、绿弯菌门（Chloroflexi）和蓝藻门（Cyanobacteria）是水稻土中优势微生物类群。四种类型土壤发育的水稻土细菌群落结构差异显著（Stress<0.001）,群落结构分异（NMDS1）与土壤pH存在极显著正相关关系（P<0.01）。土壤有机碳和碱解氮含量显著影响水稻土中细菌丰度和群落多样性（P<0.01）。红壤发育的水稻土细菌16S rRNA基因拷贝数显著高于其他三种类型水稻土,但OTU数量、Chao1指数和PD指数均低于其他三种类型水稻土。土壤pH对水稻土生物固氮速率有显著影响（P<0.01）,紫色土发育的水稻土具有最高的生物固氮速率（3.2±0.7 mg×kg^-1×d^-1）,其中优势类群细鞘丝藻属（Leptolyngbya）可能是生物固氮的主要贡献者。研究结果丰富了对水稻土微生物多样性的认识,为通过调控土壤pH和微生物群落组成来提高稻田生物固氮潜力提供了理论依据。     

Methanogenic archaeal communities developed in paddy fields in the Kojima Bay polder, estimated by denaturing gradient gel electrophoresis, real-time PCR and sequencing analyses

Methanogenic archaeal communities inhabiting the paddy field soils in the Kojima Bay polder were investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), real-time PCR and sequencing analyses. Soil samples of the plow and subsoil layers were collected in 2006 from four paddy fields that were reclaimed between 1692 and 1954. The DGGE band patterns of the targeted 16S rRNA genes amplified from the extracted DNA from the samples were different from the patterns from the paddy field soils in diluvial and alluvial areas. The numbers of targeted 16S rRNA genes, which were involved with methanogenic archaeal and other archaeal sequences, were approximately 10⁷–10⁸ and 10⁶ g⁻¹ dry soil in the plow and subsoil layers, respectively. Sequences of methanogenic archaeal 16S rRNA genes belonging to Methanocellales (Rice cluster I), Methanosarcinales and Methanobacteriales were obtained from the major DGGE bands. Whereas sequences in Methanomicrobiales, which were predominant methanogens in the diluvial and alluvial paddy fields, were not recovered. Known halophilic and methylotrophic methanogens, which are characteristic of saline and marine environments, were not detected. These results indicate that distinctive methanogenic archaeal communities have developed in the paddy field soils in the Kojima Bay polder.     

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。     

Bacterial communities and biogeochemical transformations of iron and sulfur in a high saltmarsh soil profile

Microbial community structure in saltmarsh soils is stratified by depth and availability of electron acceptors for respiration. However, the majority of the microbial species that are involved in the biogeochemical transformations of iron (Fe) and sulfur (S) in such environments are not known. Here we examined the structure of bacterial communities in a high saltmarsh soil profile and discuss their potential relationship with the geochemistry of Fe and S. Our data showed that the soil horizons Ag (oxic–suboxic), Bg (suboxic), Cr₁ (anoxic with low concentration of pyrite Fe) and Cr₂ (anoxic with high concentrations of pyrite Fe) have distinct geochemical and microbiological characteristics. In general, total S concentration increased with depth and was correlated with the presence of pyrite Fe. Soluble + exchangable-Fe, pyrite Fe and acid volatile sulfide Fe concentrations also increased with depth, whereas ascorbate extractable-Fe concentrations decreased. The occurrence of reduced forms of Fe in the horizon Ag and oxidized Fe in horizon Cr₂ suggests that the typical redox zonation, common to several marine sediments, does not occur in the saltmarsh soil profile studied. Overall, the bacterial community structure in the horizon Ag and Cr₂ shared low levels of similarity, as compared to their adjacent horizons, Bg and Cr₁, respectively. The phylogenetic analyses of bacterial 16S rRNA gene sequences from clone libraries showed that the predominant phylotypes in horizon Ag were related to Alphaproteobacteria and Bacteroidetes. In contrast, the most abundant phylotypes in horizon Cr₂ were related to Deltaproteobacteria, Chloroflexi, Deferribacteres and Nitrospira. The high frequency of sequences with low levels of similarity to known bacterial species in horizons Ag and Cr₂ indicates that the bacterial communities in both horizons are dominated by novel bacterial species.     

Changes in Mycobacterium spp. population structure and pyrene mineralization in polycyclic aromatic hydrocarbon-amended soils

The effect of pyrene and phenanthrene contamination on soil Mycobacterium spp. community structure was examined using PCR-amplification of 16S rRNA genes with primers specific for the fast-growing group of Mycobacterium spp. and separation of phylotypes by temperature gradient gel electrophoresis (TGGE). The degradative potential of the soil microbial community was measured over time by mineralization of ¹⁴C-pyrene added to the contaminated soils. PCR-TGGE profiles, in combination with band sequencing and phylogenetic analysis of the prominent phylotypes, indicated shifts in the Mycobacterium spp. community during incubation. Reductions in species diversity and enrichments of specific populations were observed in all pyrene- and phenanthrene-treated soils, in contrast to the relatively stable control soil profiles. Mineralization studies indicated the shortest acclimation periods and the highest initial rates of pyrene degradation occurred in soils pre-exposed to phenanthrene, or a mixture of phenanthrene and pyrene, for 14 weeks. Pre-exposure of soil microorganisms to a single dose of pyrene for the same length of time also decreased the acclimation period for the degradation of pyrene. Monthly application of either pyrene or phenanthrene to soils, however, resulted in an increase in pyrene degradative potential 6 weeks after the first pre-exposure, but a decrease in degradative potential 14 weeks after the first pre-exposure. Similar PCR-TGGE profiles were obtained from soils with comparable pyrene mineralization curves or degradative potentials.     

The Introduction of Woody Plants for Freshwater Wetland Restoration Alters the Archaeal Community Structure in Soil

Due to the severe degradation of wetland ecosystems in China, great efforts, such as the reconstruction of forested wetlands, have been devoted to restore the damaged and degraded wetlands to support species diversity and ecosystem services. However, less attention has been given to the diversity and ecological significance of prokaryotes of the domain Archaea compared with prokaryotes of the domain Bacteria during the reconstruction of forested wetlands. Here, the effects of introduced woody plants (Taxodium distichum and Alnus trabeculosa ) on the archaeal community in a freshwater wetland in the Yangtze estuary were investigated. The results showed that Thaumarchaeota obviously predominated at three studied sites in the freshwater wetland, the relative abundance of which decreased with increasing depth, ranging from 93.9% (0–10 cm) to 1.9% (30–40 cm) in mudflats, from 100% (0–10 cm) to 64.8% (30–40 cm) in T. distichum sediment and from 100% (0–10 cm) to 66.7% (40–50 cm) in A. trabeculosa sediment. The abundances of the archaeal amoA gene in woody plant sediments, ranging from 3.27 × 10⁷ to 2.45 × 10⁸ copies g⁻¹ dry soil, were significantly higher than those in bare mudflat, ranging from 9.23 × 10⁶ to 1.35 × 10⁷ copies g⁻¹ dry soil. The archaeal community, which was significantly affected by pH, microbial carbon and SO₄²⁻ contents according to a canonical correspondence analysis, was significantly altered by plants and soil depth (p < 0.05). These results indicated that the introduction of woody plants stimulates the proliferation of Thaumarchaeota, especially ammonia‐oxidizing archaea, which could be important contributors to the N cycle in forested wetland ecosystems. Copyright © 2017 John Wiley & Sons, Ltd.