长期施肥对稻田土壤固碳功能菌群落结构和数量的影响

微生物固碳在减缓全球气候变化、实现人类可持续发展方面具有重要的意义,通过揭示长期不同施肥制度对土壤固碳细菌的影响规律,可以为我国稻田土壤科学施肥,稻田固碳和温室气体减排的共轭双赢作用提供重要的理论依据。以湖南宁乡国家级稻田肥力变化长期定位试验为平台,采用PCR-克隆测序和实时荧光定量(Real-time)PCR技术,研究不施肥(CK),氮磷钾肥（NPK）和秸秆还田（NPKS）3种长期施肥制度对稻田土壤固碳细菌群落结构及数量的影响。通过分析固碳细菌cbbL基因文库发现,长期施肥导致土壤固碳细菌种群结构产生了明显差异,NPK和NPKS处理中兼性自养固碳菌群落优势增加而严格自养固碳菌生长受到抑制。LUBSHUFF软件统计分析显示cbbL基因文库在CK、NPK及NPKS处理间均存在显著性差异。 3种施肥处理的稻田土壤细菌cbbL基因拷贝数为3.35?108 —5.61?108每克土,施肥后,土壤细菌cbbL基因数量增加,其中NPKS处理cbbL数量最多,是CK处理的1.5倍左右。稀疏曲线则显示长期施化肥导致细菌cbbL基因多样性高于NPKS,而NPKS高于CK。上述结果表明了长期施肥对土壤固碳细菌群落结构,多样性及数量均有显著的影响。本研究结果可为深入探讨稻田土壤微生物固碳潜力及其影响机理提供有力的依据。     

Changes in bacterial CO2 fixation with depth in agricultural soils

Soils were incubated continuously in an atmosphere of ¹⁴CO₂ and the distribution of labeled C into soil organic carbon (¹⁴C-SOC) was determined at 0–1, 1–5, and 5–17 cm down the profile. Significant amounts of ¹⁴C-SOC were measured in paddy soils with a mean of 1,180.6?±?105.2 mg kg^–1 at 0–1 cm and 135.3?±?47.1 mg kg^?1 at 1–5 cm. This accounted for 5.9?±?0.7 % and 0.7?±?0.2 %, respectively, of the total soil organic carbon at these depths. In the upland soils, the mean ¹⁴C-SOC concentrations were 43 times (0–1 cm) and 11 times (1–5 cm) lower, respectively, than those in the paddy soils. The amounts of ¹⁴C incorporated into the microbial biomass (MBC) were also much lower in upland soils (5.0?±?3.6 % and 2.9?±?1.9 % at 0–1 and 1–5 cm, respectively) than in paddy soils (34.1?±?12.4 % and 10.2?±?2.1 % at 0–1 and 1–5 cm, respectively). Similarly, the amount of ¹⁴C incorporated into the dissolved organic carbon (DOC) was considerably higher in paddy soils (26.1?±?6.9 % and 6.9?±?1.3 % at 0–1 and 1–5 cm, respectively) than in upland soils (6.0?±?2.7 % and 4.3?±?2.2 %, respectively). The observation that the majority of the fixed ¹⁴C-SOC, RubisCO activity and cbbL gene abundance were concentrated at 0–1 cm depth and the fact that light is restricted to the top few millimeters of the soil profiles highlighted the importance of phototrophs in CO₂ fixation in surface soils. Phylogenetic analysis of the cbbL genes showed that the potential for CO₂ fixation was evident throughout the profile and distributed between both photoautotrophic and chemoautotrophic bacteria such as Rhodopseudomonas palustris, Bradyrhizobium japonicum, Rubrivivax gelatinosus and Ralstonia eutropha.     

Application of targeted metagenomics to explore abundance and diversity of CO2-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea

Sequestration of CO₂ by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO₂. Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed < 95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real‐time PCR (qRT PCR), was 9.38 ± 0.75 × 10⁷ and 5.43 ± 0.79 × 10⁸ (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO₂‐fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management.     

毛竹林集约经营对土壤固碳细菌群落结构和多样性的影响

为揭示毛竹集约经营对土壤固碳细菌的影响,分别采集集约经营时间为0、10、15、20年和25年的毛竹林土壤(0—20 cm和20—40 cm)土壤,应用实时荧光定量PCR、T-RFLP以及cbbL基因文库方法,分析毛竹林长期集约经营过程中土壤固碳细菌丰度和群落结构多样性的变化,通过冗余分析(RDA)探讨影响土壤固碳细菌群落的主要环境因素。结果表明,长期的集约经营显著提高了毛竹林表层和亚表层土壤的养分含量,土壤pH值却明显降低。集约经营毛竹林土壤固碳微生物数量并未表现出与SOC的相关性,而与N素水平的变化显著相关。具体表现为:随着集约经营的进行表层cbbL基因丰度呈先上升(10年)后下降的规律,与氮素水平呈正相关(P0.05);亚表层土壤cbbL基因丰度则呈直线下降的趋势,与C∶N呈正相关(P0.05)。集约经营导致表层和亚表层土壤微生物群落结构改变,表层固碳细菌多样性指数下降。由系统发育分析可知,不可培养固碳细菌占56%比例,土壤中共同的优势种类多为变形菌和放线菌,以兼性自养为主。RDA分析结果表明土壤酸化和养分积累是毛竹林土壤固碳细菌群落和多样性变化的重要原因。     

Comparison of crop productivity and soil microbial activity among different fertilization patterns in red upland and paddy soils

Soil enzyme activity and microorganism community can be changed through different long-term fertilization patterns. However, the effect of different fertilization practices on soil microorganisms might differ among crop systems. The objective of the study was to reveal the change of soil enzyme activity and soil microorganism community in different fertilizations both in upland and paddy soils. Therefore, based on long-term fertilization experiments in upland soil started in 1986 and adjacent paddy soil experiment commenced in 1981, with both consisting of 4 treatments: Control (no fertilization), N (only nitrogen fertilizer), NPK (nitrogen, phosphate and potassium fertilizers) and NPKM (nitrogen, phosphate and potassium fertilizers plus organic manure), grain yield, soil fertility, activities of soil urease, catalase, acid phosphatase, microorganism community (the number of bacteria, fungus and actinomycete) were analyzed. The result showed that: the highest grain yield was attained under the application of chemical fertilizers plus manure, as compared with Control, NPKM significantly increased the grain yield by 908.63% in corn and 118.80% in rice (p < 0.05). Meanwhile, NPKM treatment increased significantly soil organic matter and nutrient contents in upland and paddy soils. Interestingly, there was no significant difference in soil pH among all the treatments of paddy soil, but in upland, NPKM increased pH in comparison to Control by 23.06% (1.15 units of pH). Compared with Control, soil urease, catalase activities, bacteria and actinomycete numbers of NPKM were increased by 321.39%, 129.64%, 229.79%, 85.81% in upland soil, and 25.11%, 251.12%, 292.83%, 196.34% in paddy soil. However, in paddy soil, the soil acid phosphatase activity of Control, NPK and NPKM treatments were higher than upland soil by 34.87%, 44.81%, 52.73% and 30.11%. Then, the soil fungus and actinomycete numbers of paddy soil were lower than upland soil by 20.20% and 88.29%. Therefore, it indicated that long-term application of chemical and organic fertilizers delivered highest productivity in both experiment but the effect of fertilizer practices differed between land uses.     

Diversity of Green-Like and Red-Like Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes (cbbL) in Differently Managed Agricultural Soils

A PCR-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I large-subunit genes (cbbL) as a functional marker of autotrophic bacteria that fix carbon dioxide via the Calvin-Benson-Bassham cycle. We constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of cbbL genes. The diversity of these cbbL genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment. cbbL gene fragments were amplified from extracted soil DNAs, and PCR products were cloned and screened by restriction fragment length polymorphism analysis. Selected unique cbbL clones were sequenced and analyzed phylogenetically. The green-like cbbL sequences revealed a very low level of diversity, being closely related to the cbbL genes of Nitrobacter winogradskyi and Nitrobacter vulgaris. In contrast, the red-like cbbL gene libraries revealed a high level of diversity in the two fertilized soils and less diversity in unfertilized soil. The majority of environmental red-like cbbL genes were only distantly related to already known cbbL sequences and even formed separate clusters. In order to extend the database of available red-like cbbL sequences, we amplified cbbL sequences from bacterial type culture strains and from bacterial isolates obtained from the investigated soils. Bacterial isolates harboring the cbbL gene were analyzed phylogenetically on the basis of their 16S rRNA gene sequences. These analyses revealed that bacterial genera such as Bacillus, Streptomyces, and Arthrobacter harbor red-like cbbL genes which fall into the cbbL gene clusters retrieved from the investigated soils.     

Diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric CO2

Aerobic anoxygenic phototrophic bacteria (AAnPB) are recognized as an important group driving the global carbon cycling. However, the diversity of AAnPB in terrestrial environment remains largely unknown as well as their responses to the elevated atmospheric CO₂. By using culture‐independent techniques, the diversity of AAnPB in paddy soil and the changes in response to the rising atmospheric CO₂ were investigated within China FACE (Free‐air CO₂ enrichment) platform. There was a phylogenetically diverse AAnPB community with large population size residing in paddy soil. The community structure of AAnPB in bulk and rhizospheric soils stayed almost identical, while the population size was higher in rhizospheric [2.0–2.5 × 10⁸ copy number of pufM genes g^?1 dry weight soil (d.w.s.)] than that in bulk (0.7–0.8 × 10⁸ g^?1 d.w.s.) soils. Elevated atmospheric CO₂ appeared to significantly stimulate AAnPB abundance (up to 1.4–1.5 × 10⁸ g^?1 d.w.s.) and result in a higher AAnPB percentage in total bacterial community (from 0.5% up to 1.5%) in bulk soil, whereas no significant effect was observed in rhizospheric soil. Our results would extend the functional ecotypes of AAnPB and indicate that environmental changes associated with the rising atmospheric CO₂ might affect AAnPB community in paddy soil.     

Abundance and Diversity of CO<Subscript>2</Subscript>-fixing Bacteria in Grassland Soils Close to Natural Carbon Dioxide Springs

Gaseous conditions at natural CO₂ springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO₂ concentrations ([CO₂]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO₂-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavešinci mofette, a natural CO₂ spring which is known for very pure CO₂ emissions, at different distances from the CO₂ releasing vents, at locations that clearly differed in soil CO₂ efflux (from 12.5 to over 200 μmol CO₂ m⁻² s⁻¹ yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the “red-like” type of cbbL genes could be detected. In contrast, the “green-like” type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of “red-like” cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO₂ concentrations. Furthermore, the diversity pattern of “red-like” cbbL genes changed depending on the CO₂ regime. This indicates that only a part of the autotrophic CO₂-fixing microbes could adapt to the very high CO₂ concentrations and adverse life conditions that are governed by mofette gaseous regime. Urška Videmšek, Alexandra Hagn, Michael Schloter, and Dominik Vodnik contributed equally to this study.     

Metagenomic and 14C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%–82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴C-CO₂ are assimilated into SOC (74.3–175.8 mg ¹⁴C kg⁻¹) and microbial biomass (5.2–24.1 mg ¹⁴C kg⁻¹) after 45 days incubation, where more than 70% of ¹⁴C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.     

长期施肥对新疆灰漠土土壤微生物群落结构与功能多样性的影响

以20a新疆国家灰漠土土壤肥力与肥料效益长期定位试验为平台,采用常规培养法,结合Biolog技术对可培养微生物、生理菌群数量和碳源利用进行测定分析,研究撂荒(CK0)、耕作不施肥(CK)、不同化肥(N、NK、NP、PK、NPK)、化肥配施低量高量有机肥(NPKM1和NPKM2)和秸秆还田(NPKS)等10种处理土壤微生物特征,揭示长期施肥对土壤微生物群落结构与功能多样性的影响。结果表明:(1)可培养微生物:与CK处理相比,CK0处理显著提高了细菌、放线菌和真菌的数量(P0.05),NPKS处理微生物数量则显著降低(P0.05);不同化肥处理的细菌(除PK处理外)、放线菌(除PK和N处理外)数量也有所增加,增幅在8.14%—135.70%和15.30%—44.78%之间;真菌数量(除NK处理外)则有一定幅度的降低;NPKM1和NPKM2处理,微生物数量最高,细菌分别增加了162.20%和173.75%,放线菌增加了34.39%和39.37%,真菌增加了63.33%和488.33%;(2)生理菌群:与CK0相比,CK处理显著提高了自生固氮菌和亚硝化细菌数量(P0.05),显著降低了氨化细菌和纤维素分解菌数量(P0.05);与CK相比,NPKM1和NPKM2处理显著提高土壤中与氮素转化有关的生理菌群数量(P0.05),不同化肥处理和NPKS处理的影响不相同,NPK处理显著高于其余处理(P0.05);(3)微生物碳源利用:微生物活性表现为NK、NPKM1、NPKM2N、NPK、CKPK、NPKSCK0、NP;CK0处理3个多样性指数以及NPKM1、NPKM2和NK处理Shannon(H)指数最高,其余施肥处理差异不显著;糖类、氨基酸类、羧酸类和胺类是微生物利用的主要碳源。(4)聚类分析表明,除NP处理外,施氮处理土壤有较为相似的碳源利用,细菌和真菌与养分之间有较好的相关性,可培养微生物和生理菌群与微生物碳源利用的相关性较差。因此,长期不同施肥对新疆灰漠土土壤微生物群落结构和功能多样性产生了显著的影响,长期耕作不施肥降低了土壤微生物群落结构和功能多样性,不同化肥配合施用对微生物群落的影响不同,NPK及NPK配施有机肥可提高土壤微生物多样性。     

不同施肥制度土壤微生物量碳氮变化及细菌群落16S rDNA V3 片段PCR产物的DGGE分析

应用化学分析和变性梯度凝胶电泳（DGGE）技术分离PCR扩增的16S rDNA的方法,研究了不同施肥制度对土壤微生物量碳、氮变化及微生物多样性的影响。结果表明,连续15a长期试验下,土壤微生物量碳（SMB-C）和微生物量氮（SMB-N）的含量大小均为长期撂荒（CK0）土壤高于农田土壤,而在农田土壤中,长期施肥的处理（NPK、NPKM、NPKSt和NPKF）高于长期不施肥处理（CK）,不同的种植制度中,长期复种轮作（NPKF）高于长期复种连作（NPK）;各处理的SMB-C/SOC（土壤有机碳）和SMB-N/TN（全氮）的比值的变化趋势与SMB-C和SMB-N变化一致;从PCR-DGGE分析,长期氮磷钾化肥配施有机肥（NPKM）处理的微生物量碳、氮的含量最高,微生物丰度最高,细菌物种最多,其次为长期撂荒（CK0）,CK处理细菌物种最少。UPGMC聚类分析表明NPK和NPKF处理细菌的群落结构相似,CK和CK0处理细菌的群落结构相似,而NPKM和NPKSt处理细菌的群落结构相似。     

Patterns of Bacterial Diversity Along a Long-Term Mercury-Contaminated Gradient in the Paddy Soils

Mercury (Hg) pollution is usually regarded as an environmental stress in reducing microbial diversity and altering bacterial community structure. However, these results were based on relatively short-term studies, which might obscure the real response of microbial species to Hg contamination. Here, we analysed the bacterial abundance and community composition in paddy soils that have been potentially contaminated by Hg for more than 600 years. Expectedly, the soil Hg pollution significantly influenced the bacterial community structure. However, the bacterial abundance was significantly correlated with the soil organic matter content rather than the total Hg (THg) concentration. The bacterial alpha diversity increased at relatively low levels of THg and methylmercury (MeHg) and subsequently approached a plateau above 4.86 mg kg^?1 THg or 18.62 ng g^?1 MeHg, respectively. Contrasting with the general prediction of decreasing diversity along Hg stress, our results seem to be consistent with the intermediate disturbance hypotheses with the peak biological diversity under intermediate disturbance or stress. This result was partly supported by the inconsistent response of bacterial species to Hg stress. For instance, the relative abundance of Nitrospirae decreased, while that of Gemmatimonadetes increased significantly along the increasing soil THg and MeHg concentrations. In addition, the content of SO₄ ^2?, THg, MeHg and soil depth were the four main factors influencing bacterial community structures based on the canonical correspondence analysis (CCA). Overall, our findings provide novel insight into the distribution patterns of bacterial community along the long-term Hg-contaminated gradient in paddy soils.     

Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes

A molecular approach, based on the detection of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit genes, was applied to investigate the distribution and diversity of autotrophic bacteria in groundwater systems. DNA extracts from 48 sampling stations, including a variety of pristine and polluted, shallow and deep-subsurface groundwater samples obtained from Germany and Austria, served as a template for the PCR amplification of form I (cbbL) and form II (cbbM) large subunit RubisCO genes. The majority of the samples (>80%) contained two different forms of RubisCO. In 17 samples, all three forms of RubisCO were identified. PCR products from four selected groundwater habitats containing all three forms of RubisCO were used to construct clone libraries. Based on restriction fragment length polymorphism (RFLP) analysis, 109 RubisCO-clone-inserts were subjected to sequencing and phylogenetic analysis. With the exception of a form IA RubisCO sequence cluster obtained from deep subsurface samples, which was identical to the RubisCO genes described for Ralstonia metallidurans CH34, most sequences were distantly related to a variety of RubisCO species in chemolithoautotrophic Proteobacteria. Several sequences occurred in isolated lineages. These findings suggest that autotrophic bacteria with the capability to assimilate CO₂ via the Calvin Cycle pathway are widespread inhabitants of groundwater systems.     

黄泥田土壤真菌群落结构和功能类群组成对施肥的响应

研究长期不同施肥黄泥田土壤真菌群落组成和功能特性,深入认识真菌对不同施肥的响应机理,可以为合理施肥和保证农田土壤健康发展提供科学依据.设置不施肥(CK)、单施无机肥(NPK)、无机肥配施农家肥(NPKM)、无机肥加秸秆还田(NPKS)4个处理,采用Illumina高通量测序和FUNGuild对不同施肥处理下黄泥田土壤真菌群落结构和功能群进行分析.结果表明:从门水平上看,土壤真菌群落主要由子囊菌、担子菌和接合菌构成,且以子囊菌为主(47%~74%).NPKM和NPKS处理中子囊菌的相对丰度分别为49%和47%,显著低于CK(71%)和NPK(74%)处理,从目水平上看,减少的主要为肉座菌、格孢腔菌和散囊菌.NPKM和NPKS处理担子菌相对丰度分别为18%和28%,高于CK(14%)和NPK(10%)处理,从目水平上看,增加的主要为银耳菌、糙孢伏革菌和伞菌.与CK相比,单施无机肥降低了担子菌含量.不同施肥处理均在一定程度上增加了接合菌门的丰度,从目水平看,以内囊霉菌和粪蛙霉菌为主.NPK处理真菌α多样性指数显著低于其他处理,NPKM和NPKS处理的丰富度指数(Chao1和ACE)高于CK和NPK处理.不同处理之间真菌的营养类型以腐生营养型为主(48%~57%),NPKM和NPKS处理的共生营养型真菌相对丰度为17%,显著高于CK和NPK处理,增加的以丛枝菌根真菌、外生菌根真菌为主.NPK处理动物病原菌含量(10%)显著高于其他处理.冗余分析(RDA)结果表明,土壤含水量、孔隙度和盐度是影响真菌群落结构和功能类群组成的主要因子,其次为有机质和总氮.长期单施无机肥降低真菌种群多样性,增加致病菌含量,不利于土壤健康,而有机无机肥配施可在一定程度上提高真菌种群丰富度指数和共生真菌比例,有利于保持黄泥田稻田土壤健康的生态环境和真菌群落的多样性.     

RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage

The enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-six cbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of cbbL and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.     

长期施肥对土壤微生物量及土壤酶活性的影响

 该文以北京国家褐潮土土壤肥力与肥料效益长期监测基地的长期肥料定位试验为平台,研究了长期不同施肥制度对土壤的生物学特性及其土壤酶的影响。主要研究结果：长期撂荒土壤(15年)的有机质和全氮(TN)的含量、微生物量碳(SMB-C)和氮(SMB-N)、土壤的蔗糖酶、磷酸酶和脲酶活性以及SMB-C/SOC(土壤有机碳)和SMB-N/TN比值都高于种植作物的农田土壤;而其代谢商和容重值低于农田土壤。长期施肥的农田(NPK、NPKM 、NPKS和NPKF),其土壤养分含量、微生物量碳和氮以及土壤蔗糖酶、磷酸酶和脲酶活性均高于不施肥的农田(CK);而小麦(Triticum aestivum)-玉米(Zea mays)→小麦-大豆(Glycine max)复种轮作(NPKF)的农田又高于长期复种连作(NPK)的农田;在施肥处理中(NPK、NPKM、NPKS和NPKF),长期化肥与有机肥配合施用的处理(NPKM )的土壤上述指标高于其它施肥处理(NPK、NPKS和NPKF),但其土壤的代谢商、pH值和容重值较低。     

Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities

Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO₂ concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.     

Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette

Effects of extremely high carbon dioxide (CO₂) concentrations on soil microbial communities and associated processes are largely unknown. We studied a wetland area affected by spots of subcrustal CO₂ degassing (mofettes) with focus on anaerobic autotrophic methanogenesis and acetogenesis because the pore gas phase was largely hypoxic. Compared with a reference soil, the mofette was more acidic (ΔpH ∼0.8), strongly enriched in organic carbon (up to 10 times), and exhibited lower prokaryotic diversity. It was dominated by methanogens and subdivision 1 Acidobacteria, which likely thrived under stable hypoxia and acidic pH. Anoxic incubations revealed enhanced formation of acetate and methane (CH₄) from hydrogen (H₂) and CO₂ consistent with elevated CH₄ and acetate levels in the mofette soil. ¹³CO₂ mofette soil incubations showed high label incorporations with ∼512 ng ¹³C g (dry weight (dw)) soil⁻¹ d⁻¹ into the bulk soil and up to 10.7 ng ¹³C g (dw) soil⁻¹ d⁻¹ into almost all analyzed bacterial lipids. Incorporation of CO₂-derived carbon into archaeal lipids was much lower and restricted to the first 10 cm of the soil. DNA-SIP analysis revealed that acidophilic methanogens affiliated with Methanoregulaceae and hitherto unknown acetogens appeared to be involved in the chemolithoautotrophic utilization of ¹³CO₂. Subdivision 1 Acidobacteriaceae assimilated ¹³CO₂ likely via anaplerotic reactions because Acidobacteriaceae are not known to harbor enzymatic pathways for autotrophic CO₂ assimilation. We conclude that CO₂-induced geochemical changes promoted anaerobic and acidophilic organisms and altered carbon turnover in affected soils.     

秸秆还田对玉米根际氨氧化微生物群落及红壤硝化潜势的影响

为探讨酸性红壤根际氨氧化微生物群落以及硝化作用对不同秸秆还田处理的响应,基于中国科学院鹰潭红壤生态实验站设置的秸秆还田长期试验平台(9年),采用荧光定量PCR和高通量测序技术,研究不同秸秆还田处理(不施肥(CK);氮磷钾肥(NPK);氮磷钾肥+秸秆(NPKS);氮磷钾肥+秸秆猪粪配施(NPKSM);氮磷钾肥+秸秆生物炭(NPKB))下玉米根际土壤氨氧化古菌(ammonia-oxidizing archaea, AOA)和细菌(ammonia-oxidizing bacteria, AOB)丰度和群落结构的变化,揭示了秸秆还田对根际氨氧化微生物群落结构和硝化潜势(potential nitrification activity, PNA)的影响机制。结果发现：相比CK和NPK处理,秸秆还田显著提高了土壤养分含量和硝化潜势,其中有机碳(SOC)、全氮(TN)、全磷(TP)、速效磷(AP)、速效钾(AK)、硝态氮(NO~-₃-N)和铵态氮(NH~+₄-N)含量显著增加,NPKSM处理对土壤肥力提升效果最佳。AOA的硝化潜势显著高于AOB,表明AOA...