酸性红壤上玉米不同部位固氮微生物群落丰度和组成特征

  【目的】   发挥微生物固氮功能可降低农田化学氮肥的投入,对于缓解土壤酸化具有重要意义。固氮微生物广泛存在于植物体的各个部位,了解酸性土壤上作物不同部位固氮微生物群落特征,为挖掘其功能潜力提供数据支撑和理论基础。   【方法】   选择性状差异较大的耐铝玉米品种先玉335和铝敏感品种Mo17为试验材料,在酸性红壤上种植1个月后,收集玉米地上部、根部和根际土壤样品,分析玉米生物量、养分含量和根际土壤基本理化性质;采用实时荧光定量PCR和高通量测序技术,以nifH基因为标靶,分析不同玉米品种、不同取样部位 (叶部、根部和根际土壤) 固氮微生物群落的丰度、多样性和结构组成。   【结果】   先玉335地上和地下生物量显著高于Mo17,但是植株氮、磷浓度和根际土壤pH、铵态氮和速效钾含量却低于Mo17。实时荧光定量PCR结果显示,nifH基因丰度在玉米不同部位间的差异程度明显大于玉米品种间的差异,其中根部丰度显著高于根际土壤和叶部,而且先玉335根部nifH基因丰度要高于Mo17。高通量测序分析显示,变形菌门 (Proteobacteria) 和蓝藻门 (Cyanobacteria) 是固氮微生物的优势门,根际土壤和根部的优势菌属是慢生根瘤菌属 (Bradyrhizobium),而叶部优势菌属是细鞘丝藻属 (Leptolyngbya),多数优势菌属相对丰度在玉米不同部位间呈现显著差异。取样部位显著影响固氮微生物群落多样性指数 (Shannon指数和OTU数量),但同一部位品种间没有明显差异,其中根际多样性指数显著高于根部,两者均高于叶部。非度量多维尺度 (NMDS) 和PERMANOVA分析显示,取样部位对固氮微生物群落结构组成的影响程度显著高于品种的影响,根际土壤、根部和叶部三者之间的群落组成差异达到显著水平,而品种间仅仅根际土壤样品差异显著。   【结论】   酸性红壤上,玉米不同部位间的固氮微生物群落丰度、多样性和结构组成差异程度显著高于品种间的差异。根部固氮微生物丰度最高,暗示固氮潜力更大。叶部固氮微生物群落组成显著不同于根际土壤和根部,且有最低的丰度和多样性,这与叶片苛刻的环境条件密切相关。     

长期施肥下红壤旱地解钾菌变化及其驱动因子

在南方红壤区,研究长期施肥下土壤解钾菌的变化规律及其驱动因素,可为该地区土壤钾素资源管理和钾肥合理施用提供理论依据。基于红壤旱地长期定位施肥试验(始于1986年),选取不施肥(CK)、施氮磷肥(NP)、氮磷钾肥(NPK)和氮磷钾肥配施有机肥(NPKM)处理,分析玉米开花期根际土壤的解钾菌类型和解钾能力及其有机酸和激素含量,并结合玉米根系特性和根际土壤理化性质探讨影响红壤旱地解钾菌变化的关键因子。结果表明:与NPK处理相比,NPKM处理的根长、根表面积、根直径和根体积分别增加了112.3%、174.4%、32.43%和291.5%,根际土壤pH提高了0.67个单位,有机质、非交换性钾和交换性钾分别增加了29.50%、19.34%和53.89%。各施肥处理根际土壤中均存在解钾菌,CK和NP处理的解钾菌均为类芽孢杆菌属,NPK和NPKM处理则均为纤维菌属。与CK处理相比,NP、NPK和NPKM处理下根际土壤解钾菌的解钾效率分别增加了162.4%、139.0%和105.6%,其中NP处理解钾菌的解钾效率最高。偏最小二乘路径模型的结果显示,根系和施肥可同时调控解钾菌的解钾效率。冗余分析(RDA)进一步表明,根系长度和表面积与土壤解钾菌特性呈显著正相关关系(P0.05)。因此,红壤旱地长期不同施肥措施不仅直接影响玉米根系发育特征和根际土壤理化性质,还能显著改变土壤解钾菌群落及其解钾能力,其中根系长度和表面积是调控玉米根际土壤中解钾菌的关键因子。     

聚乙烯微塑料对玉米根际土壤微生物群落结构的影响

为了研究聚乙烯类微塑料对玉米根际土壤微生物群落结构的影响,以玉米为试材,以平均分子量为2000、5000、10万的聚乙烯粉末模拟土壤中的微塑料污染,设置5个处理:不添加聚乙烯(CK)、添加分子量为2000(T1)、5000(T2)、10万以上(T3)的聚乙烯且种植玉米、未添加聚乙烯未种植玉米(CK0),分析玉米抽穗期各部位矿质元素代谢和根际土壤微生物群落结构差异。结果显示,矿质元素含量在玉米各部位存在差异,Fe、Cu主要集中在玉米根部, Ca、Mn、Mg在叶中分布最多, K主要集中在茎中;添加不同分子量聚乙烯微塑料后,不同部位的矿质元素较CK增加,且T1处理下增加最多。微生物多样性分析显示,不同分子量聚乙烯微塑料对玉米根际微生物群落组成影响不同。T1处理下除变形杆菌纲、伯克氏菌科细菌丰度增加外,其他细菌丰度较CK均减少;T3处理下,细菌和真菌的丰度较CK都有较大幅度的增加。总体来看,添加聚乙烯后,玉米不同部位矿质元素含量较CK显著增加, 2000分子量聚乙烯能够显著降低土壤中细菌和真菌的丰度, 10万以上分子量聚乙烯使得土壤中细菌和真菌丰度增加,各处理中与环境污染物降解相关的微生物增多。     

磷肥对酸性红壤上玉米不同部位丛枝菌根真菌群落的影响

为了研究不同磷肥水平下酸性红壤上玉米不同部位丛枝菌根真菌(Arbuscular mycorrhizal fungi, AMF)群落多样性和组成结构,明确玉米不同部位AMF群落的分布特征及对磷肥的响应差别,为提高酸性红壤磷素利用提供理论依据。本实验设置三个磷肥水平：不施磷、低磷(25 mg P /kg)和高磷(100 mg P /kg),玉米培养4周后,测定玉米生物量和土壤理化性质,利用高通量测序技术检测玉米根部、根际和非根际土壤AMF群落结构和多样性。结果显示,随着磷肥水平增加,玉米生物量显著提高,高磷处理下玉米地上部磷含量显著高于不施磷和低磷处理。取样部位(根部、根际和非根际)显著影响了AMF群落优势属球囊霉属(Glomus)、巨孢囊霉属(Paraglomus)和近明球囊霉属(Claroideoglomus)相对丰度,但是磷肥影响不显著。类似的,取样部位而不是磷肥显著影响了AMF群落香农指数和物种丰富度。非度量多维标度(NMDS)结果显示,根部样品与非根际和根际土壤样品群落距离更远,而相同取样部位中不同磷肥水平间群落组成更为相似；置换多元方差分析(PERMANOVA)进一步表明,取样部位而不是磷肥显著影响了AMF群落组成结构,主要表现在根部样品与根际和非根际土壤不同。因此,酸性红壤上玉米不同部位对AMF群落的影响明显高于磷肥作用,表明AMF应用于酸性红壤时应重点考虑作物部位的特性。     

再生水灌溉对4类土壤Cd生物有效性的影响

根据国家土壤环境质量标准,选取重金属Cd含量为二级水平的4类土壤（红壤、 潮土、 土、 黑土）进行土培试验,研究再生水灌溉与小白菜生物量及Cd含量、 土壤有效态Cd含量、 pH、 微生物群落的关系,以及不同类型土壤间的差异性。结果表明, 再生水灌溉在不同类型土壤上对小白菜生物量及Cd含量、 土壤有效态Cd含量、 土壤pH和微生物数量的影响不同: 1）红壤、 潮土、 土上小白菜生物量增加显著,分别增加9.09%、 16.08%、 9.92%,黑土上增加不显著; 2）小白菜Cd含量在红壤上显著降低,由对照的0.29 mg/kg降低到0.22 mg/kg,在黑土上比对照增加了18.75%,在潮土和土上影响不大; 3）有效态Cd含量在红壤没有变化,但在潮土、 土、 黑土上增加显著; 4） 4类土壤微生物数量增加显著; 5）潮土、 土、 黑土的pH值有所降低。     

PGPR菌剂对辣椒的促生效应及根际土壤细菌的响应研究

研究田间条件下PGPR菌剂灌根对辣椒根际土壤细菌数量及群落结构的影响,为深入探究PGPR菌剂的田间促生机制提供理论依据。以4株PGPR菌株制成PGPR菌剂,对辣椒进行灌根,并采用Illumina-MiSeq平台对辣椒根际土壤细菌V3-V4区进行Paired-end测序,结合细菌及功能菌群数量、辣椒产量指标,比较分析菌剂灌根配施全量化肥(PGPR-CF1)、菌剂灌根配施80%化肥(PGPR-CF2)和全量化肥(CK)处理后对辣椒根际土壤细菌数量及群落结构特征的影响。结果表明:PGPR菌剂灌根后辣椒根际土壤细菌及包含固氮、解磷及解钾等功能菌群的数量显著提高,且物种丰度和多样性均高于对照,细菌优势度则表现为PGPR-CF1和CK组高于PGPR-CF2。所有土样共得到有效序列573 896条,在相似水平为97%下聚类分析得到OTUs数分别为2 153个(CK)、2 337个(PGPR-CF1)、2 358个(PGPR-CF2);各处理辣椒根际土壤中的优势门为酸杆菌门、放线菌门、拟杆菌门、绿弯菌门、浮霉菌门和变形菌门,相对丰度总占比分别为83.7%(PGPR-CF1)、79.55%(PGPR-CF2)和79.77%(CK)。PGPR菌剂灌根后增加了伯克霍尔德氏菌目、芽孢杆菌目、鞘脂单胞菌目等的相对丰度,降低了芽单胞菌目、酸杆菌目的相对丰度。Pearson指数表明,辣椒产量和单果重与根际土壤细菌多样性和丰度正相关。研究显示,PGPR菌剂处理,可以提高根际土壤细菌和功能菌群的数量,同时影响了物种多样性和群落结构,并促进了辣椒增产。     

氮形态和磷肥对红壤玉米根际解磷微生物群落和磷酸酶活性的影响

较低的土壤磷素有效性限制了酸性红壤生产潜力提升。作为磷素活化的主要执行者,解磷微生物对施肥和根际作用的综合响应尚不清楚。以玉米为试验材料,设置磷肥水平（施磷和不施磷）与不同氮形态（铵态氮肥和硝态氮肥）的交互试验,使用编码酸性磷酸酶和碱性磷酸酶的微生物phoC和phoD基因作为分子标记物,研究了施肥和根际作用对酸性红壤磷酸酶活性和相关功能微生物群落的影响。结果显示,根际作用显著提高了土壤磷酸酶活性,且作用强度大于氮形态和磷肥水平。氮形态、磷肥水平和根际作用均显著影响phoD细菌操作分类单元（OTU）数目和香农指数,然而仅有氮形态和根际作用影响phoC细菌OTU数目。根际作用对phoC和phoD细菌群落组成结构的影响程度显著高于氮形态和磷肥水平,而且对phoD细菌群落的作用更明显。根际磷酸酶活性提高与土壤有机质增加密切相关。phoC细菌群落组成和结构的变化主要与根际养分变化有关,而phoD细菌群落结构的变化可能是根系分泌物和养分变化共同作用的结果。总体而言,玉米根际作用对酸性红壤磷酸酶活性和相关功能细菌群落的影响大于氮形态和磷肥水平,但是其作用强度一定程度上依赖于上述施肥措施。     

生物质炭负载解钾菌对土壤酶活性与微生物群落结构的影响

为探究生物质炭负载解钾菌对土壤微生物特性的影响,基于5个处理即空白（CK）、施用化学钾肥（KCl）、接种解钾菌（KSB）、施用生物质炭（BC）、施用生物质炭负载解钾菌（BC-KSB）的黑麦草盆栽耗竭试验,分析不同处理下土壤酶和微生物群落结构的响应特征。结果表明,BC-KSB相比其余施肥处理更有利于提高土壤脲酶、蔗糖酶、酸性磷酸酶和过氧化氢酶的活性,同时也提高了土壤细菌的物种多样性与菌群丰富度,并提高了土壤有益菌群（绿弯菌门、放线菌门、芽孢杆菌属和慢生根瘤菌属）的丰度,抑制了土壤致病菌群（变形菌门和罗河杆菌属）的繁殖。各施肥处理相比CK均显著提升了黑麦草干物质量,且以BC-KSB处理对黑麦草干物质量的提升最为显著。与CK和KCl相比,BC-KSB能显著提高土壤微生物生物量碳、微生物生物量氮、有机质、全氮和速效钾的含量（P <0.05）。冗余分析表明,土壤有机质、速效钾、酸性磷酸酶、脲酶和微生物生物量氮是影响细菌群落结构的主要因子,黑麦草的生长主要受伯克氏菌属和罗河杆菌属的影响较大。可见,BC-KSB对黑麦草产量、土壤养分、土壤酶活性和细菌群落结构均产生了积极的影响,对于改良土壤生态...     

生物有机肥对烟草根际微生物群落及青枯雷尔氏菌丰度的影响

【目的】探究生物有机肥施用对烟草根际土壤细菌、真菌群落结构和青枯雷尔氏菌丰度的影响机理。【方法】选用长沙市某公司生产的生物有机肥和常规烟草专用肥,在湘西花垣县长期定位试验点连续5年开展大田试验,研究施肥对土壤理化性质和微生物群落的影响。试验设置两种施肥处理：常规烟草专用肥（CF）和生物有机肥（BOF）。【结果】与CF相比,施用生物有机肥处理的土壤烟草青枯病发病率降低了89.8%,同时青枯雷尔氏菌相对丰度也显著降低,降幅达40.1%;土壤pH、碱解氮和有效磷显著增加,分别增加了1.2%、12.1%和60.2%;施用生物有机肥后根际土壤微生物如Roseiflexaceae,Gemmatimonadaceae,Nitrospira,Ramophialophora,Preussia等显著富集,且这些潜在有益菌与青枯雷尔氏菌相对丰度呈显著负相关关系。通过ABT预测模型分析发现潜在有益菌是影响青枯雷尔氏菌相对丰度的最主要生物因子。【结论】连续5年的试验结果表明,施用生物有机肥不仅改善了作物生长的土壤环境,显著提高了土壤pH和土壤速效养分含量,还促使潜在有益菌在根际土壤中富集,抑制了青枯雷尔氏菌的生...     

基于高通量测序的木薯根域土壤微生物群落结构研究

为研究木薯根域土壤微生物群落结构,开展了根袋试验,处理包括2个木薯品种(华南205:SC205和桂热4号:GR4)和3个施肥处理(包括不施肥T1,普通施肥T3,施2倍氮肥T7),并进行了Illumina Hiseq高通量测序。结果表明,细菌优势群落为放线菌门(Actinobacteria,8.579%～10.697%),变形菌门(Proteobacteria)、绿弯菌门(Chloroflexi)等。根域土壤比非根际土壤相对富集变形菌门和10个细菌属;SC205根域的硝化螺旋菌门(Nitrospirae)、5个纲(δ变形菌纲等)和6个属(Flavisolibacter等)的相对丰度比GR4要高,但鞘脂杆菌纲则相反。真菌优势群落为子囊菌门(43.71%～59.79%)、毛霉门、担子菌门等。根域土壤施肥抑制壶菌门(Chytridiomycota)相对丰度。相对于根域土壤,T7提高了非根际土壤中的Agaricomycetes, Geminibasidiomycetes和Microbotryomycetes纲的相对丰度。T7比T1显著降低了根域土壤Chytridiomycetes纲的相对丰度。LEfSe结果表明:根域土壤施肥降低了哈茨木霉的相对丰度。α多样性结果表明:土壤细菌物种丰度顺序为T7 GR4T7 SC205和T7 soil。T3真菌物种丰度比T7高,T7真菌Chao1指标比T1低。结论:GR4根域土壤细菌物种丰度、硝化螺旋菌门和5个纲、6个属的相对丰度都小于SC205,品种间细菌差异暗示氮转化过程和根系分泌物的差异。施肥降低了真菌物种丰度。壶菌门和4个真菌纲、哈茨木霉受施肥或根系影响,暗示它们与肥料或者根系分泌物的交互作用。本研究为深入认知木薯根际微生物提供了基础。     

Potential of wild species for genetic enhancement of some semi-arid food crops

Discovery and incorporation of genes from wild species provide means to sustain crop improvement, particularly when levels of resistance in the cultigens are low and virulent strains of pests and pathogens overcome the host plant resistance. The extent of utilization and the potential of the wild genepool for genetic enhancement were reviewed in five important food crops viz. sorghum, pearl millet, chickpea, pigeonpea and groundnut grown in the semi-arid tropics. Introgression from compatible wild germplasm in the primary gene pool resulted in transfer of new cytoplasmic male sterility systems in pearl millet and pigeonpea, development of high protein, cleistogamous flower and dwarf pigeonpea lines and foliar disease resistant groundnut cultivars. Utilization of wild species in secondary and tertiary gene pools has been generally limited due to sterility, restricted recombination or cross incompatibility. Nevertheless, these species are extremely important as they contain high levels of resistance to several important biotic and abiotic stresses. Several of them, like those belonging to the Parasorghum section and the rhizomatous Arachis species are sources of multiple resistances and hold great promise to sustain crop productivity.     

“绿色革命”以来大气CO2浓度升高对C3作物营养品质的影响

自20世纪60年代"绿色革命"以来,育种技术和农耕技术的发展促进了农作物产量的大幅提升,然而作物的营养品质出现下降趋势。在相似的遗传背景下,大气CO_2浓度升高会使单位体积农作物产品的营养元素含量下降,因此"绿色革命"至今,农作物产品的营养元素下降可能受大气CO_2浓度升高影响。通过植物生长箱模拟"绿色革命"初期和目前的大气CO_2浓度水平(310μmol/mol和400μmol/mol),针对主要C_3作物水稻、小麦和大豆,研究"绿色革命"以来大气CO_2浓度升高对其籽粒的C、N、Fe、Zn元素含量的影响,结果表明:CO_2浓度升高对3种作物籽粒的C元素含量几乎没有影响,变化幅度在±1.5%之间;籽粒的N、Fe、Zn元素含量普遍呈现下降趋势,但均未达到显著水平。     

Faculty positions:Center for Agricultural Resources Research,Chinese Academy of Sciences

正The Center for Agricultural Resources Research(CARR),the Institute of Genetics and Developmental Biology(IGDB),Chinese Academy of Sciences,invites applicants for several research group leader positions.CARR is one of the research organizations in Chinese Academy of Sciences(CAS).We seek nominations and applications     

Collection and preliminary evaluation of native turfgrass accessions in Italy

Despite a raising interest on turfs in Italy, all theavailable varieties of this kind in the Country are of foreign origin, and areoften poorly adapted to the prevailing climatic conditions. This prompted tobegin a collection activity of indigenous turfgrass species, with the ultimategoal of identifying promising materials for future breeding based on localgenetic resources. The collection was carried out in three areas of Italy, viz.the northern Po Plain, the coastal region of Liguria, and the island of Sardiniathat are characterised, respectively, by subcontinental, warm temperate, andtypical Mediterranean climate. Altogether, 141 sites were visited, yielding 226accessions belonging to eight species of potential interest for turfs:Poa pratensis, Poa trivialis,Festuca rubra, Festuca arundinacea,Lolium perenne, Agrostis stolonifera,Agrostis tenuis, and Cynodon dactylon,this last being a warm-season grass. Poa pratensis andCynodon dactylon were mostly collected in northern Italyand Sardinia, respectively, whereas Festuca arundinacea andLolium perenne were rather ubiquitous. The collection sitesranged from 0 to 1040 m asl, but sites over 750 m wereonly visited in the inner part of Sardinia. All the accessions, collected aswhole plants, were transplanted at Lodi, northern Italy, where they are beingevaluated. Their preliminary evaluation for traits of importance for turf use,such as sward colour and overall quality, highlighted the great variation andthe occurrence of interesting accessions in all species. Other characters wererecorded, bearing specific importance in individual species, and in all casespromising accessions were identified. The germplasm of Festucarubra, Festuca arundinacea, and Loliumperenne proved highly infected by endophytic (symbiotic) fungi of thegenus Neotyphodium.     

Leaf position and genotype differences for mineral element concentrations in sorghum grown on tropical acid soil 1

Mineral element deficiencies and toxicities are common problems associated with sorghum [Sorghum bicolor (L.) Moench] production on acid soils. To better understand some of the mineral element problems and the analysis of plant tissue of sorghum plants grown on acid soils, four sorghum genotypes were grown on an acid Oxisol at Carimagua, Colombia limed with dolomite at 2 and 6 Mg ha^‐1.

Samples for mineral element analyses were obtained from leaves at different positions on the four genotypes. Concentrations of P and Mg were highest in the flag leaf (Leaf No. 1) and decreased as the position on the plant declined from the top of the plant for plants grown at 2 Mg lime ha^‐1. Similar decreases in P, Mg, K, and Zn concentrations occurred in plants grown with 6 Mg lime ha^‐1. Concentrations of Ca, S, Si, Mn, Fe, Cu, and Al increased as leaf position declined from the flag leaf for plants grown at 2 and 6 Mg lime ha^‐1. The higher lime supply enhanced Ca and reduced Mn and Fe concentrations in leaves. Differences in mineral element concentrations for the four genotypes used were fairly extensive. The elements to show the greatest range among genotypes were Al and Si and the elements to show the least range among genotypes were P, K, and S. Care should be used in collecting leaf samples for plant analysis and genotypic differences for accumulation of mineral elements should be considered in interpretation of results.     

Short-term variation in the concentration of selected ions within individual tropical rainstorms

Rainwater was collected at the campus of the University of Brunei Darussalam in Bandar Seri Begawan, Brunei Darussalam, using a funnel-in-bottle sampler. Polypropylene bottles were changed at intervals during rainstorm events. The pH and conductivity were determined immediately after collection on aliquots of the sample. Samples were refrigerated at 5°C for subsequent chemical analysis. Analyses for Na, Mg, Ca, Zn and Fe were carried out by means of inductively coupled plasma atomic emission spectroscopy (ICP-AES); Cu and Mn were analysed by graphite furnace atomic absorption spectroscopy (GFAAS); K was analysed using flame atomic emission spectroscopy (FAES); and Cl^–, NO₃ ^– and SO₄ ^2– were analysed by ion chromatography (IC). Concentration versus time profiles are reported for three rainstorm events. All ions exhibited a decrease in concentration during the rainstorm. The first sample contained the highest concentration of ions, consistent with a first-flush effect. The contribution of the initial stages of the shower to the total quantity of ion deposited during the entire rainstorm is quite overwhelming; in many cases 20 to 30% of the mass was deposited in less than 5% of rainstorm duration. On the other hand, the pH and conductivity variation during rainstorms did not exhibit a consistent pattern.     

Leaf litter selection by detritivore and geophagous earthworms

Summary Litterbag experiments with 10 different kinds of leaf litter showed that detritivore (Lumbricus species) and geophagous (Aporrectodea species) earthworms prefer certain litter types over others, since different numbers of worms were found below the litter after 50–52 days of exposure in a pasture. The detritivores preferred Fraxinus, Tilia, and predecomposed Ulmus and Fagus litter to Fagus litter and paper, while geophages preferred Tilia litter to Alnus and Ulmus litter, so that the two groups of earthworms showed different preferences. The detritivores seemed to be more selective than the geophages. The palatability of the litter was examined in relation to the C: N ratio, the lignin concentration and the initial and final polyphenol concentration. The numbers of detritivores were significantly correlated with the C: N ratio and the final polyphenol concentration, so that selection of litter seems to be related to palatability. The numbers of geophages were not significantly correlated with any of the parameters for palatability. The disappearance of litter after 50–52 days appeared to be due to detritivore activity, since the numbers found below the litter were positively and significantly correlated with the litter disappearance. There was no significant correlation with geophage activity. This indicates that detritivores use litter as food, and therefore influence the composition of the litter layer.     

The 5S rRNA gene diversity in the genus <Emphasis Type="Italic">Secale</Emphasis> and determination of its closest haplomes

We analyzed 127 rDNA sequences (5S DNA units) obtained from 23 seed accession samples from more or less 10 taxa in wild and cultivated rye, genus Secale L. The sequences fell into two known groups, here assigned to two unit classes, viz. long R1 and short R1 (designations to reflect on R haplome of rye). The different taxa could not be fully differentiated based on the 5S DNA units. We searched for 5S DNA sequences from known unit classes most closely similar to the long R1 and the short R1. One set with the long R1 unit class contained sequences of the long P1 unit class from Agropyron (P haplome) and from Kengyilia (StYP haplome), long J1 from Thinopyrum (J haplome), whereas the set with the short R1 included the long S1 from Pseudoroegneria (St haplome) and Kengyilia (StYP haplome), the short J1 from Thinopyrum (J haplome) and the short V1 from Dasypyrum (V haplome). Each of the two sets was analyzed separately by maximum likelihood (ML) phylogenetic analysis from which we were able to infer that the 5S DNA units of Secale differentiated in a non-clock fashion and followed the HKY substitution model in the gene tree with the long R1 unit class and the HKY + G in the gene tree with the short R1 unit class. A complementary Bayesian analysis yielded identical tree topologies to the ML ones for each of the two sequence sets. In the tree with the long R1 units the long P1 and long J1 unit classes were closest to the long R1 unit class, whereas in the tree with the short R1 units the long S1 and short J1 unit classes were closest to the short R1 unit class, indicating possibly a close relationship between the St, J and R haplomes.     

Nematode succession and microfauna-microorganism interactions during root residue decomposition

The quality of plant material affects the vigor of the decomposition process and composition of the decomposer biota. Root residues from hairy vetch (Vicia villosa Roth), rye (Secale cereale L.) and vetch+rye, packed in litterbags were placed in pots of soil at 15 C and the content of the bags was analyzed after 2, 4, 8 and 12 weeks. Bacterial biomass did not differ between residues with contrasting composition. Among bacterivores groups of nematodes that require high bacterial production dominated in fast decomposing resources whereas flagellates with smaller requirements prevail in slower decomposing resources. Biomass of bacterial feeding nematodes correlated positively with early phase (0-2 wk) decomposition that increased in the order: rye< vetch+rye<vetch. Bacterial biomass therefore seems to be under top-down (predation) control during early decomposition. In contrast, the fungal biomass differed between resources with highest values for rye. Moreover, this increase in fungal biomass occurred later during succession and was correlated with decomposition activity for rye in that period. Fungal biomass therefore seems to be under bottom-up (resource) control. The composition of the nematode assemblages (composed of 25 taxa) showed a clear relationship to initial plant resource quality as well as decomposition phase. Early successional microbivorous nematodes vary according to resource quality with demanding bacterivores+predators (Neodiplogasteridae) dominating in vetch and less demanding bacterivores (Rhabditidae) and fungivores (Aphelenchus) being equally common in vetch and rye. Later in the succession (2-4 wk) bacterivorous Cephalobidae and fungivorous Aphelenchoides prevailed similarly on the different root materials whereas bacterivorous protozoa and the amoebal fraction thereof dominated in rye. At week 12 no species dominated the nematode assemblages that were similar between the resources. The differences between nematode assemblages among plant resources at 2 week were similar to the results of a field study sampled after 6 weeks with the same soil and plant resources. This lends support to the relevance of the successional patterns observed in this incubation study.     

Cycling of extracellular DNA in the soil environment

Upon entering the soil environment, extracellular DNA is subjected to dynamic biological, physical, and chemical factors that determine its fate. This review concerns the fate of both recombinant and non-recombinant sources of DNA. A schematic of DNA cycling coupled with genetic transformation is presented to understand its behavior in soil. Extracellular DNA may persist through cation bridging onto soil minerals and humic substances, be enzymatically degraded and restricted by DNases of microbial origin, and/or enter the microbial DNA cycle through natural transformation of competent bacteria. Lateral gene transfer may disseminate DNA through the microbial community. An understanding of DNA cycling is fundamental to elucidating the fate of extracellular DNA in the soil environment.