Long-term fertilization regimes affect bacterial community structure and diversity of an agricultural soil in northern China

Background, Aims, and Scope  Knowledge about shifts of microbial community structure and diversity following different agricultural management practices could improve our understanding of soil processes and thus help us to develop sound management strategies. A long-term fertilization experiment was established in 1989 at Fengqiu (35°00′N, 114°24′E) in northern China. The soil (sandy loam) is classified as aquic inceptisols and has received continuous fertilization treatments since then. The fertilization treatments included control (CK, no fertilizer), chemical fertilizers nitrogen (N) and potassium (K) (NK), phosphorous (P) and K (PK), NP, NPK, organic manure (OM), and half chemical fertilizers NPK plus half organic manure (1/2NPKOM). The objective of this study was to examine if the microbial community structure and diversity were affected by the long-term fertilization regimes. Materials and Methods  Soil samples were collected from the long-term experimental plots with seven treatments and four replications in April 2006. Microbial DNAs were extracted from the soil samples and the 16S rRNA genes were PCR amplified. The PCR products were analyzed by DGGE, cloning and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and the clone libraries constructed from the excised DGGE bands. Results  The bacterial community structure of the OM and PK treatments were significantly different from those of all other treatments. The bacterial community structures of the four Ncontaining treatments (NK, NP, NPK and 1/2NPKOM), as well as CK, were more similar to each other. The changes in bacterial community structures of the OM and PK treatments showed higher richness and diversity. Phylogenetic analyses indicated that Proteobacteria (30.5%) was the dominant taxonomic group of the soil, followed by Acidobacteria (15.3%), Gemmatimonadetes (12.7%), etc. Discussion  Irrespective of the two fertilization treatments of OM and PK, the cluster analysis showed that bacterial communities of the remaining five treatments of CK, NK, NP, NPK and 1/2NPKOM seemed to be more similar to each other, which indicated the relatively weak effects of the four N-containing treatments on soil bacterial communities. N fertilizer may be considered as a key factor to counteract the effects of other fertilizers on microbial communities. Conclusions  Our results show that long-term fertilization regimes can affect bacterial community structure and diversity of the agricultural soil. The OM and PK treatments showed a trend towards distinct community structures, higher richness and diversity when compared to the other treatments. Contrasting to the positive effects of OM and PK treatments on the bacterial communities, N fertilizer could be considered as a key factor in the soil to counteract the effects of other fertilizers on soil microbial communities. Recommendations and Perspectives  Because of the extremely high abundance and diversity of microorganisms in soil and the high heterogeneity of the soil, it is necessary to further examine the effects of fertilization regimes on microbial community and diversity in different type soils for comprehensively understanding their effects through the appropriate combination of molecular approaches. ESS-Submission Editor: Chengrong Chen, PhD (c.chen@griffith.edu.au)     

华北山前平原农田土壤养分循环的酶学调控

土壤酶是推动土壤养分循环的生物催化剂, 研究华北山前平原农田养分循环的酶学调控机制将有助于评价该地区土壤养分状况。试验用土壤取自中国科学院栾城农业生态系统试验站, 分析了土壤脲酶与碱性磷酸酶活性在0~10 cm、10~20 cm、20~30 cm 和30~40 cm 4 个土层中的分布, 研究了土壤粗砂(2 000~200 μm)、粉砂(200~63 μm)、粉粒(63~2 μm)和黏粒(2~0.1 μm) 4 个颗粒组中土壤酶活性与土壤养分之间的相关性。研究结果表明: 土壤脲酶活性与碱性磷酸酶活性均随土壤深度增加而降低, 土壤酶活性随土壤粒径减小而升高。在土壤粗砂和粉砂组分中, 土壤酶活性与养分含量显著相关, 而在土壤粉粒和黏粒组分中, 土壤酶活性与土壤养分含量并不总是显著相关。这些结果说明: 土壤酶活性在土壤养分循环中起到重要的调控作用, 土壤粗砂和粉砂中的土壤酶具有较高的田间实际催化活性, 对土壤养分循环的贡献较大; 与此相反, 土壤粉粒和黏粒中的土壤酶由于土壤无机矿物的吸附作用而失去部分田间催化能力, 降低了其对土壤养分循环的贡献。     

Single particle analysis reveals that bacterial community structures are semi-specific to the type of soil particle

Abstract

With the aim of understanding how diverse bacteria are distributed within a heterogeneous soil, we compared local bacterial communities on individual soil particles. We picked up 11 coarse sand-sized particles (quartz, whitish feldspar, yellow feldspar or unidentified brown particles) from a sandy soil, extracted DNA from each particle, and carried out partial 16S rDNA polymerase chain reaction denaturing gradient gel electrophoresis analysis. Bacterial communities located on soil particles of the same type were more similar in composition than communities located on particles of the other types. Thus, the local structure of a bacterial community is related to the type of soil particle, which suggests that a high diversity of soil bacteria emerges through a combination of local bacterial communities on different types of soil particles.     

Changes in soil bacterial community structure and microbial function caused by straw retention in the North China Plain

ABSTRACT

The effects of straw retention on soil bacterial community structure, microbial function, and biochemical properties were assessed. Terminal restriction fragment length polymorphism (T-RFLP) and community-level physiological profile (CLPP) assays were used to assess the bacteria community structure and microbial function respectively. Treatments included straw removal with conventional tillage (CT), straw retention with conventional tillage (SRCT) and straw retention with no tillage (SRNT). SRCT and SRNT significantly (p < 0.05) increased soil organic carbon by 8.9% and 9.7%, and microbial biomass carbon by 44.7% and 330.8%, respectively, compared with CT. T-RFLP analysis indicated that straw retention had no favourable effect on soil bacterial diversity, and SRCT significantly (p < 0.05) decreased bacterial diversity compared to CT. Among the three treatments, SRNT had the highest activity of urease, invertase, cellulase, and β-glucosidase. SRCT significantly (p < 0.05) increased the activity of invertase and β-glucosidase compared to CT treatment. CLPP analysis showed that microbial functional diversity was significantly (p < 0.05) increased by straw retention. Enzyme activity and microbial functional diversity were not correlated with bacterial diversity. Therefore, according to this study, SRNT is a better farming practice because it improves soil fertility and biological quality.     

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.     

接种自生固氮菌对玉米根际土壤酶活性和细菌群落功能多样性的影响

为了探索玉米根际土壤微生态特征对接种自生固氮菌的响应机理,在盆栽实验条件下,研究了3株自生固氮菌褐球固氮菌（Azotobacter chroococcum YCYS）、芸苔叶杆菌（Phyllobacterium brasssicacearum QL54）和类芽孢杆菌（Paenibacillus sabinae MX31）接种盆栽玉米（Zea mays L.）之后,玉米根际土壤酶活性和细菌群落功能多样性的变化。结果表明,接种自生固氮菌对玉米根际土壤酶活性和细菌群落功能多样性产生了一定的影响,而且不同自生固氮菌之间的接种效果有一定的差异。接种褐球固氮菌（A. chroococcum YCYS）和类芽孢杆菌（P. sabinae MX31）玉米根际土壤脲酶活性分别比对照高20.55%和9.58%。然而接种处理对玉米根际土壤碱性磷酸酶活性的影响差异不显著（P0.05）。BIOLOG结果显示,接种自生固氮菌可以提高细菌总代谢活性,其中接种褐球固氮菌（A. chroococcum YCYS）处理的AWCD是对照的1.8倍,并且细菌群落丰富度指数（R）显著高于对照（P0.01）。不同接种处理土壤根际细菌生理碳代谢优势群落结构不同。主成分分析（PCA）表明接种自生固氮菌可以调控根际土壤细菌群落功能多样性。     

不同深度土壤控水对稻田土壤微生物区系及细菌群落多样性的影响

为研究不同深度土壤控水对壤土稻田土壤水势、微生物区系和细菌群落多样性的影响,通过土培池栽试验,在水稻生育后期设置土壤深度0~5 cm（S05）、0~10 cm（S10）和0~15 cm（S15）控水处理,以保持水层为对照,分析了不同深度控水处理下5 cm、10 cm、15 cm深土壤水势与土壤微生物区系、细菌群落多样性的变化。结果表明：土壤5 cm、10 cm、15 cm深度的水势随着控水深度增加而降低,S05控水处理主要影响上层（5 cm）土壤水势,S10控水处理影响上、中层（10 cm）土壤水势,S15控水处理土壤水势随土层深度的增加而升高。花后8 d和32 d,S05控水处理上层土壤细菌数量显著高于S10、S15控水处理;花后16~24 d,S05控水处理中层、下层（15 cm）土壤细菌数量均显著高于S15控水处理;土壤水势与水稻生育后期中、下层土壤细菌数量呈极显著正相关关系。S05控水处理10 cm、15 cm土层的细菌丰富度Chao指数均显著高于S15控水处理及CK。3个控水处理中,5 cm土层细菌的多样性Shannon指数以S05控水处理最低。优势细菌菌群分析发现,优势群落主要为变形菌门、绿弯菌门、酸杆菌门、拟杆菌门,四者总相对丰度在80%以上;S15控水处理中层土壤变形菌门相对丰度低于S05和S10控水处理。3个控水处理土壤样品中优势纲（相对丰度大于2%）达15个,主要包括α-变形菌纲、β-变形菌纲、δ-变形菌纲、厌氧绳菌纲等,这4个纲的总相对丰度在47%以上,其中厌氧绳菌纲相对丰度最高;上层土壤中S05控水处理的β-变形菌纲相对丰度显著低于S10和S15控水处理。因此,不同深度土壤控水对壤土土壤水势、细菌数量存在影响,改变了细菌的多样性及丰富度,对土壤细菌优势菌种类无显著影响。     

毒死蜱对棉花根际土细菌群落多样性和结构的影响

通过室内盆栽试验模拟自然环境条件,采用高效液相色谱(HPLC)和末端限制性片段长度多态性(T-RFLP)技术,研究了土壤使用推荐剂量(5 mg·kg~(-1))及推荐剂量的2倍、3倍和4倍(10 mg·kg~(-1)、15 mg·kg~(-1)、20 mg·kg~(-1))毒死蜱对棉花根际土壤细菌群落多样性和结构的影响,以不施用毒死蜱的土壤为对照。结果表明,5 mg·kg~(-1)、10 mg·kg~(-1)、15 mg·kg~(-1)和20 mg·kg~(-1)毒死蜱在土壤中的半衰期分别为10.04 d、11.36 d、11.55 d和12.16 d,60 d时基本完全降解。毒死蜱处理60 d后,棉花生物量显著降低;毒死蜱浓度越高,棉花生物量越低。无毒死蜱条件下不同取样时间根际细菌多样性无显著差异,毒死蜱处理组前30 d细菌多样性均显著降低,60 d时毒死蜱处理组细菌多样性恢复到正常水平。研究发现毒死蜱浓度越高对细菌多样性抑制作用越显著,恢复越缓慢。主成分分析结果发现,第10 d、30 d和60 d毒死蜱处理组与对照组细菌群落结构差异显著,其中60 d时20 mg·kg~(-1)毒死蜱处理组差异最显著,即使土壤中毒死蜱完全降解,根际细菌群落结构仍不会恢复到正常水平。60 d时,被毒死蜱抑制的细菌有硝化刺菌属(Nitrospina sp.)和Cellulophaga sp.等,被激活的有芽孢杆菌属(Bacillus sp.)和链霉菌属(Streptomyces sp.)等。可见,毒死蜱的引入,重新构建了土壤细菌群落结构,显著影响棉花生长,对棉花根际土壤微生态环境冲击较大,应对其生态安全性予以重视。     

模拟增温和降水调控对土壤微生物碳氮、群落基质利用模式及群落组成的短期影响

Soil microorganisms are major drivers of soil carbon(C) cycling;however,the response of these microorganisms to climate change remains unclear.In the present study,we investigated how 18 months of multifactor climate treatments(warmed air temperature by 3℃ and decreased or increased precipitation manipulation by 30%) affected soil microbial biomass C and nitrogen(N),community substrate utilization patterns,and community composition.Decreased and increased precipitation significantly reduced microbial biomass C by 13.5% and 24.9% and microbial biomass N by 22.9% and 17.6% in unwarmed plots,respectively(P0.01).Warming enhanced community substrate utilization by 89.8%,20.4%,and 141.4% in the natural,decreased,and increased precipitation plots,respectively.Particularly,warming significantly enhanced the utilization of amine and carboxylic acid substrates among all precipitation manipulation plots.Compared with the natural air temperature with natural precipitation treatment,other treatments affected fungal community richness by -0.9% to 33.6% and reduced the relative abundance of the dominant bacterial and fungal groups by 0.5% to 6.8% and 4.3% to 10.7%,respectively.The warming and/or precipitation manipulation treatments significantly altered Zygomycota abundance(P0.05).Our results indicate that climate change drivers and their interactions may cause changes in soil microbial biomass C and N,community substrate utilization patterns,and community composition,particularly for the fungal community,and shifts in the microorganism community may further shape the ecosystems function.     

连续施用解磷菌肥对复垦土壤磷酸酶和Hedley磷形态的影响

为了研究增施解磷菌肥对土壤供磷状况的改善和土壤中磷有效性的提高状况,通过田间小区试验研究了连续施用解磷菌肥对复垦5年土壤碱性磷酸酶活性及Hedley磷形态的影响。结果表明:施用无机肥+有机肥+解磷菌肥处理的土壤碱性磷酸酶活性最高,为30.65μg/(g·h),比对照提高了83.86%。本试验年与第3年复垦土壤相比,土壤中Hedley磷形态的含量都有不同程度的增加,H_2O-Po含量以无机肥+有机肥+解磷菌肥处理为最高,比对照提高了93.90%;NaOH-Pi、HCl-Pi、HCl-Po含量以无机肥+解磷菌肥处理最大,分别比对照提高了194.2%、61.87%、105.8%;残渣态磷含量以无机肥处理影响最大,比对照提高了22.87%;H_2O-Pi、NaHCO_3-Po含量以有机肥处理最大,比对照提高了129.2%、85.89%;NaHCO_3-Pi、NaOH-Po含量以有机肥+解磷菌肥处理提高最大,分别提高了176.9%、114.4%。可以得出:施用解磷菌肥的处理增加复垦土壤中H_2O-Po、NaHCO_3-Pi、NaOH-Pi、NaOH-Po、HCl-Pi、HCl-Po含量的效果较好。H_2O-Pi、H_2O-Po、NaHCO_3-Pi、NaHCO_3-Po、NaOH-Pi、NaOH-Po、HCl-Pi与碱性磷酸酶均呈极显著相关。解磷菌肥在一定程度上增强了复垦土壤碱性磷酸酶活性,影响土壤中Hedley磷分级的各形态磷素含量,从而提高磷的有效性。     

土壤微生物群落结构与多样性对农田集约化管理程度降低的响应

Using a scheme of agricultural fields with progressively less intensive management （deintensification）, different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage （CT） or no-tillage （NT）, an organic farming system （OR）, an integrated cropping system with animals （IN）, a successional field （SU）, and a plantation woodlot （WO）. Microbial phospholipid fatty acid （PLFA） profiles and substrate utilization patterns （BIOLOG ECO plates） were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N （P 〈 0.05） were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system （P 〈 0.05）. There were also significant decreases （P 〈 0.05） along with agricultural deintensification for contributions of total bacterial and gram positive （G＋） bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.     

北方山区主要森林类型树木叶片氮、磷回收效率研究

养分回收是植物养分利用策略的重要驱动力,可减少养分流失,降低其对环境的依赖性,对植物种群和群落稳定性、生态系统养分循环都具有重要的生态学意义。本文在收集北方山区(黄土高原、太行山区、京北山区)天然林、人工林等各种森林成熟叶片和凋落物氮、磷养分含量等资料的基础上,根据群落生活型和管理方式将各类森林进行归并,对其养分回收效率进行了综合评估。结果表明,各类森林植被通过成熟叶片和落叶中氮、磷含量计算得到的叶片氮、磷回收效率分别是24.5%~71.3%和18.1%~75.4%,均值分别是45.5%和47.4%。北方山区天然林和人工林成熟叶片的平均氮含量分别是11.6 g·kg~(-1)和21.6 g·kg~(-1),人工林成熟叶片氮含量显著高于天然林,养分在人工林生长过程中可能基本处于消耗状态。不同地区天然林与人工林叶片磷含量存在差异:太行山区天然林成熟叶片和枯落叶片磷含量显著高于人工林,而京北山区人工林成熟叶片磷含量较高,枯落叶片磷含量较低。灌木成熟和枯落叶片中氮含量显著高于乔木,而两者间磷含量无显著差异;灌木叶片氮回收效率高于乔木。通过3个地区的比较发现,京北山区树木叶片氮、磷回收效率分别是62.1%和67.8%,高于其他两个地区。相关分析表明,北方山区森林枯落叶片氮含量是影响叶片氮、磷回收效率的重要因子。通过对不同树种养分回收效率的比较发现,针叶树种养分回收效率大于阔叶树种,这说明在土壤养分贫瘠山区针叶树种的养分回收效率更高,更能适应这种贫瘠的土壤环境。在山区进行人工建植时,针叶树种高的养分利用效率应该被考虑进来。     

华北潮土长期施肥对土壤跳虫群落的影响

通过试验研究了河南封丘潮土长期施肥处理下土壤跳虫的群落结构及其多样性,试验包括氮磷钾(NPK)、氮磷(NP)、氮钾(NK)、磷钾(PK)、有机肥(OM)、1∶1化学氮肥与有机氮(MNPK)和不施肥(CK)7个处理。结果表明,7种施肥试验处理下,平均土壤跳虫密度为30 000头m-2,施用有机肥显著增加了土壤跳虫数量,而磷肥可能是该地区跳虫数量增长的一个限制因素。OM和MNPK处理下土壤跳虫多样性显著高于其他处理,OM和NPK处理具有最高的相似性,其次是MNPK和OM处理之间,而CK处理与其他处理相似性指数较小。不同施肥处理下表现了土壤跳虫类群对环境的选择性,多数跳虫与OM处理成正相关关系,而MNPK处理促进了Isotoma和Xenylla属在数量上的增长,PK处理与Hypogastrura和Sminthurinus属有一定的正相关关系。施肥处理也引起了土壤跳虫的垂直分布差异,MNPK、NPK和OM处理下土壤跳虫趋于表层(0～10cm)分布,而NK和CK处理下趋于下层(10～20cm)分布。土壤跳虫的量化指标(如个体数、类群数和多样性)对施肥处理表现敏感,可作为土壤质量评价的指标之一。     

Dose-dependent effect of compost amendment on soil bacterial community composition and co-occurrence network patterns in soybean agroecosystem

ABSTRACT

This study aimed to elucidate the effects of various doses of compost amendment on bacterial community compositions and co-occurrence network patterns across the growing season in black soil, Northeast China. Bacterial richness was unaffected by compost addition in seedling and flowering stage, whereas significantly enhanced by high level of compost addition (45,000 kg ha^?1) in mature stage. Non-metric multidimensional scaling analysis revealed distinct bacterial communities in response to compost addition across the growing season. At phylum level, copiotrophic groups of bacteria including Bacteroidetes and Firmicutes gradually increased in relative abundance along with compost rate, while oligotrophic groups (Planctomycetes and Verrucomicrobia) showed opposite tendency. Notably, these enrichment or reduction was most pronounced in seedling stage. Abundant genera including Actinomadura, Aminobacter, Cellvibrio, Devosia, Luteimonas, Microbacterium, Nonomuraea, Promicromonospora were positively and consistently correlated with compost rate, whereas Arthrobacter, Flavisolibacter, Janthinobacterium, Kaistobacter negatively correlated. Network analysis indicated that compost amended soils (40.0, 49.0, and 64.0%) harbored more positive links than control (37.6%). In addition, the soil bacterial network connectivity and connectedness generally increased along with the compost rate, while modularity exhibited opposite trend. Overall, our findings show that compost addition modified the bacterial community compositions and network patterns in soybean agroecosystem in Northeast China.     

接种溶磷真菌对玉米和大豆根际细菌群落结构多样性的影响

Application of phosphate-solubilizing microorganisms （PSMs） has been reported to increase P uptake and plant growth. However, no information is available regarding the ecological consequences of the inoculation with PSMs. The effect of inoculation with phosphate-solubilizing fungal （PSF） isolates Aspergillus niger P39 and Penicillium oxalicum P66 on the bacterial communities in the rhizospheres of maize （Zea mays L. ‘Haiyu 6＇） and soybean （Glycine max Merr. ‘Heinong 35＇） was examined using culture-dependent methods as well as a culture-independent method, polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE）. Compared with the control, the number of culturable microbes for soybean was significantly greater with P39, whereas for maize, the same was significantly greater with P66. In addition, a greater number of microbes were found in the rhizosphere of maize compared with soybean. The fingerprint of DGGE for 16S rDNA indicated that inoculation with PSF also increased bacterial communities, with the P66 treatment having higher numbers of DGGE bands and a higher Shannon-Weaver diversity index compared with P39; the composition of the microbial community was also more complex with the P66 treatment. Overall, complex interactions between plant species and exotic PSMs affected the structure of the bacterial community in the rhizosphere, but plant species were more important in determining the bacterial community structure than the introduction of exotic microorganisms.     

玉米秸秆生物炭对褐土微生物功能多样性及 细菌群落的影响

生物炭施入土壤被认为是一种有效的固碳减排措施,可增加土壤有机碳及矿质养分含量,提高土壤的持水能力及保肥能力。为探明其施入土壤后对土壤微生物活性及多样性的影响,本文在盆栽试验条件下,采用Biolog与高通量测序相结合的方法,研究了CK(不施生物炭)和施用5 g·kg~(-1)、10 g·kg~(-1)、30 g·kg~(-1)、60 g·kg~(-1)玉米秸秆生物炭对土壤微生物碳源利用能力(AWCD)、功能多样性指数以及土壤细菌的丰度和多样性的影响。结果表明,随着生物炭施用量的增加,表征土壤微生物活性的AWCD值呈下降趋势,表现为:5 g·kg~(-1)处理≈CK10 g·kg~(-1)处理30 g·kg~(-1)处理60 g·kg~(-1)处理,其中CK和5 g·kg~(-1)处理间差异不显著(P0.05),而10 g·kg~(-1)、30 g·kg~(-1)和60 g·kg~(-1)处理在整个培养期间的AWCD值显著低于CK处理(P0.05);土壤微生物群落代谢功能多样性指数(H′)、碳源利用丰富度指数(S)均随生物炭施用量的增加而呈下降趋势,但均匀度指数(E)表现出相反趋势,5g·kg~(-1)、10 g·kg~(-1)、30 g·kg~(-1)、60 g·kg~(-1)各处理的H′较CK处理分别增加0.16%、-0.88%、-3.14%、-11.09%,S分别增加-2.82%、-11.27%、-18.31%、-47.89%,E分别增加1.14%、3.00%、3.73%和13.76%。主成分分析表明,与CK处理比较,5 g·kg~(-1)处理对土壤微生物群落碳源利用方式没有显著影响(P0.05),而10 g·kg~(-1)、30 g·kg~(-1)和60g·kg~(-1)处理对土壤微生物群落碳源利用方式影响显著(P0.05)。随着生物炭施用量的增加,土壤细菌OTU数目及丰富度指数(Chao1)呈增加趋势,5 g·kg~(-1)处理与CK处理差异不显著,而10 g·kg~(-1)、30 g·kg~(-1)、60 g·kg~(-1)处理的OTU数目较CK处理分别增加1.09%、5.26%、24.42%,Chao1分别增加5.73%、10.21%、37.68%。土壤中施用生物炭后土壤细菌变形菌门(Proteobacteria)的丰度在CK处理和5 g·kg~(-1)处理间差异不显著(P0.05),而10g·kg~(-1)、30 g·kg~(-1)、60 g·kg~(-1)处理较CK处理分别增加32.3%、21.1%、16.7%,拟杆菌门(Bacteroidetes)的丰度随着生物炭施用量的增加各处理较CK处理分别减少22.1%、55.3%、66.8%、50.5%。生物炭施入土壤后降低了土壤可培养微生物的活性,减少或改变了土壤微生物碳源利用的种类,使土壤原有微生物群落组分发生改变,生物炭也影响了土壤细菌各菌群在土壤中的丰度,使其分布的均匀性降低。为了不影响微生物群落结构和功能,石灰性褐土上生物炭一次还田量不能超过5 g·kg~(-1)(干土)。     

Dynamics of extracellular DNA decomposition and bacterial community composition in soil

Microbial necromass is an important source of stabilized organic matter in soil, yet the decomposition dynamics of necromass constituents have not been adequately characterized. This includes DNA, a nutrient-rich molecule that when released into the environment as extracellular DNA (eDNA) can be readily used by soil microorganisms. However, the ecological relevance of eDNA as a nutrient source for soil microorganisms is relatively unknown. To address these deficits, we performed a laboratory experiment wherein soils were amended with ¹³C-labeled eDNA and clay minerals known to interact with DNA (kaolinite and montmorillonite). The amount of eDNA-carbon remaining in the soil declined exponentially over time. Kaolinite amendment decreased eDNA decomposition rates and, after 30 days, retained a higher fraction of eDNA-carbon (∼70% remaining) than control or montmorillonite soils (∼40% remaining), indicating that clay mineral sorption can stabilize eDNA-derived carbon in soil. Sequencing of bacterial 16S rRNA genes showed that during the incubation the relative abundance of the added eDNA's sequence decreased by 98%, 92% and 99% in the control, montmorillonite, and kaolinite amended soils respectively. These results suggest that the fraction of eDNA-carbon that remained in the soil was incorporated into microbial biomass, firmly bound to soil constituents, or fragmented and no longer amenable to sequencing. In addition, the eDNA amendment affected the composition of the bacterial community. Specifically, the relative abundance of select phyla (Planctomycetes and TM7) and genera (e.g., Arthrobacter and Nocardioides) were elevated in soils that received eDNA, suggesting these groups may be particularly effective at degrading eDNA and using it for growth. Taken together, these results indicate that while eDNA is consumed by bacteria in soil, a fraction of eDNA material is resistant to decomposition, particularly when stabilized by soil minerals, suggesting a substantial amount of recalcitrant eDNA could accumulate over time.     

Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies

Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m² sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminal-restriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m² sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.