基于分子生物学的堆肥功能微生物种群与体系基质特性关系研究
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摘要
农业废物堆肥化过程中细菌和真菌种群是堆肥微生物的重要组成成分。它们的种群组成及动态变化与堆肥化过程中各理化因子密切相关。目前学者对堆肥基质中不同的理化因子对细菌和真菌等微生物群落的影响大小及显著性缺乏整体的认识。因此判断不同理化因子对细菌和真菌等微生物种群得影响大小及显著性对于我们优化堆肥工艺、提高堆肥效率意义重大。本研究选用稻草秸秆、菜叶、土壤和麸皮等原料按照11:3:8:2比例（干重）均匀混合模拟农业废物堆肥，使用聚合酶链式反应-变性梯度凝胶电泳（PCR-DGGE）技术研究了堆肥化过程中细菌、真菌的种群动态变化特征。对细菌和真菌DGGE图谱去除背景噪音后进行条带匹配分析，以条带在不同泳道中亮度峰值的百分含量构建细菌和真菌的物种组成矩阵。使用Canoco4.5软件对获得的细菌、真菌种群数据与堆肥过程因子进行冗余分析（redundancy analysis，RDA）。结果显示，这些过程因子分别解释了73.2%和75.5%的细菌和真菌种群的变化。细菌种群组成的动态变化与WSC、铵态氮和硝态氮显著相关。它们分别解释了19.5%（P=0.002）、14.1%（P=0.004）和8.5%（P=0.002）的细菌种群组成。堆体温度、WSC和含水率显著影响真菌种群组成。它们分解解释了17.0%（P=0.002）、11.8%（P=0.002）和8.5%（P=0.01）的真菌种群数据。这些过程因子的有效调控对于优化农业废物堆肥过程中细菌和真菌的降解活性，进而促进堆肥的顺利完成具有重要意义。
氨是堆肥材料中主要的微生物可利用性含氮化合物，氮素的损失形式之一是氨的挥发。微生物将氨氧化为亚硝酸盐是硝化作用的限速步骤，决定着堆肥体系氮素得转移转化平衡。堆肥体系细菌和古细菌均具有编码氨单加氧酶的amoA功能基因，负责将氨转化为羟胺，完成堆肥体系氨的最终生物氧化。目前学界对氨氧化细菌和氨氧化古细菌在堆肥体系中的存在特征及在多大程度上影响堆肥体系氮素得转移转化平衡缺乏认识。本研究主要采用编码氨氧化菌的氨单加氧酶的amoA基因PCR-DGGE技术和荧光定量聚合酶链式反应（real-time PCR）技术，并结合堆肥基质的潜在硝化能力，比较农业废物堆肥过程中氨氧化古细菌和氨氧化细菌对堆肥基质硝化能力的贡献能力差异。结果显示，在每单位样品干重中，潜在硝化活性取值变化范围是29.3~89.9ng NO2-/(g min)。在堆肥2~6d内收集到的样品体现最高的硝化活性。随着高温期的到来，堆肥基质潜在硝化能力迅速降低，在腐熟期潜在硝化能力进一步增加，堆肥结束时达到66.1ng NO2-/(g min)。氨氧化古细菌和氨氧化细菌对堆肥理化参数的响应存在差异。古细菌amoA基因在整个堆肥进程中均有存在，主要来自于土壤/沉积物聚类（soil/sedimentcluster），这些物种与Candidatus Nitrososphaera gargensis等氨氧化古细菌有很近的遗传距离。而细菌的amoA基因仅在堆肥升温期和腐熟期检测到，全部属于亚硝化单孢菌属（Nitrosomonas），这些基因序列与欧洲亚硝化单孢菌（Nitrosomonas europaea）、Nitrosomonas communis/nitrosa等文献报道较多的已分离鉴定的亚硝化单孢菌发育关系最为接近。堆肥高温期和降温期过高的堆体温度和氨氮含量严重抑制了氨氧化细菌的种群活性。另外，氨氧化古细菌和细菌amoA基因DGGE图谱显示，古细菌amoA基因多样性在堆肥高温期达到最大值，而堆肥基质的潜在硝化能力同时达到峰值。潜在硝化能力PAO和古细菌amoA基因丰度之间存在显著正相关（R2=0.554， P<0.001），氨氧化古细菌对微生物氨氧化的功能主导作用主要发生在高温期和降温期。氨氧化细菌与堆肥基质潜在硝化活性同样显著正相关（R2=0.503，P=0.03），但这种对氮素转移转化的驱动作用主要体现在升温期和腐熟期。
木质纤维素因为结构复杂能够抵御微生物的生物降解作用，严重减缓了废物的堆肥化降解速度。大量研究表明，通过添加某些木质纤维素降解菌剂，可以有效地促进堆肥体系木质纤维素等难降解有机物的生物降解，提高堆肥效率并最终改善堆肥产品质量。黄孢原毛平革菌（Phanerochaete chrysosporium）是目前为止发现的降解木质素成分能力最强的一种白腐真菌（white-rot fungi）。近年来学者主要关注于P. chrysosporium接种对堆肥体系腐熟度指数、酶活、木质素降解速率和重金属毒性的钝化等影响。然而，我们对接种P. chrysosporium对农业废物堆肥化体系本土细菌和真菌种群的影响仍然知之甚少。采用不同阶段接种黄孢原毛平革菌（P. chrysosporium），设置4个堆肥体系，分别编号为Run A、Run B、Run C和Run D，每个体系设有3个平行。其中Run A作为没有接种P.chrysosporium的菌丝体的控制体系；Run B仅在堆肥的一次发酵阶段（2d）接种了1%的P. chrysosporium菌丝体（湿重/堆肥原料干重，下同）；Run C仅在二次发酵阶段（20d）接种了1%的P. chrysosporium菌丝体；Run D在一次发酵阶段和二次发酵阶段均接种1%的P. chrysosporium菌丝体。我们采用荧光定量PCR、克隆文库构建和PCR-DGGE等分子生物学技术研究不同P. chrysosporium的接种方式，及这些方式引起的基质异质性对农业废物堆肥体系本土细菌和真菌种群的影响。采用回归分析（regression analysis）、冗余分析（RDA）和方差分离（variance partition analysis）等多元分析方法计算和判定这些因素的影响大小及显著性。结果表明，不同P. chrysosporium接种方式显著改变了堆体基质的堆体温度、氨态氮、硝态氮、WSC、pH和C/N等参数；不同接种处理的堆体半纤维素、纤维素与木质素的降解率最终达到堆肥结束时的50%、45%和40%。在二次发酵阶段接种P. chrysosporium对木质素降解的促进作用更加明显。 P.chrysosporium接种对细菌种群丰度具有一定的刺激作用。一次发酵阶段和二次发酵阶段接种P. chrysosporium的堆体16S rDNA基因数量均显著高于未接种堆体。这也许说明，低分子量的有机物质被P. chrysosporium产生的各种胞外酶作用后释放到堆肥基质中，进而刺激了本土细菌种群的生长和代谢。细菌16S rDNA基因数量与堆体温度、铵态氮显著正相关，而与硝态氮显著负相关。不同P.chrysosporium接种策略下细菌种群组成与C/N、堆体温度和WSC显著相关。方差分离分析结果显示，它们分别解释了7.9%（P=0.03）、7.7%（P=0.026）和7.5%（P=0.034）的细菌种群组成。不同接种方式引起的堆肥基质条件变化（35.1%，P=0.002）对细菌群落的影响比接种本身（20.5%，P=0.048）更大。这些结果表明P. chrysosporium菌剂主要通过提高堆体温度、改善基质营养物质的可利用性和改变其他参数的方式来影响堆肥体系本土细菌群落的数量及组成。
克隆测序和系统发育树构建结果表明，20个堆肥样品共获得956个有效测序结果，分属于13种真菌物种。不同P. chrysosporium接种方式下的堆肥样品本土优势真菌为子囊菌门的产黄顶孢霉（Acremonium chrysogenum）、白地霉（Galactomyces geotrichum）和嗜热节格孢霉（Scytalidium thermophilum）等真菌。担子菌门的灰盖鬼伞（Coprinopsis cinerea）和未定地位真菌（Fungi incertaesedis）的奥古斯塔被孢霉（Mortierella angusta）在堆肥样品中也大量存在。枝状枝孢霉（Cladosporium cladosporioides）、隐球酵母菌（Cryptococcuspodzolicus）、 Cystofilobasidium macerans、德巴利酵母菌（Debaryomycesnepalensis）、阿姆斯特丹散囊菌（Eurotium amstelodami）、稻黑孢霉（Nigrosporaoryzae）与小不整球壳菌（Plectosphaerella cucumerina）数量较少，仅在堆肥初期存在（1d~7d）。一次发酵阶段未接种P. chrysosporium的堆体真菌丰度显著高于接种处理的堆体。在二次发酵阶段，真菌种群总数与本土真菌数逐渐降低，不同处理间没有显著差异。二次发酵阶段接种的外源白腐真菌P. chrysosporium能够比较顺利的完成在堆肥基质中的定殖与生长，其数量占总真菌总数的17.8~26.7%。堆肥初始样品本土真菌组成与后期样品差异明显，这一差异主要是由堆肥温度的变化所引起。二次发酵阶段接种显著改变了本土真菌种群组成。二次发酵阶段接种的堆体本土优势真菌物种主要为产黄顶孢霉（A. chrysogenum）和白地霉（G. geotrichum）；而未接种的堆体其本土优势真菌物种主要为枝状枝孢霉（C. cladosporioides）和嗜热节格孢霉（S. thermophilum）。回归分析显示本土真菌种群数量与C/N、WSC显著正相关，而与硝态氮显著负相关。冗余分析表明本土真菌种群的动态变化与C/N、含水率和硝态氮显著相关。 P.chrysosporium接种改变了堆肥基质的C/N、含水率和硝态氮等因素，进而影响本土真菌种群结构与丰度。
Bacteria and fungi species play significant roles in the decomposition andmineralization of agricultural organic wastes during composting. Their communitycompositions are likely influenced by several physico-chemical parameters incomposting systems. So far, the physico-chemical parameters have not beenevaluated simultaneously with the bacterial and fungal composition changes toseparate out their relative importance. It is of interest to conduct such research todetermine to what extent of differences in bacterial and fungal communities areinfluenced by these parameters, respectively. The goal of this study was to identifyand prioritize some of the physico-chemical parameters that contributed to bacterialand fungal community compositions during agricultural waste composting. Ricestraw, vegetables, soil and bran were homogenized at a ratio of11:3:8:2to simulateagrcultural wastes composting. Bacterial and fungal community compositions weredetermined by polymerase chain reaction-denaturing gradient gel electrophoresis(PCR-DGGE). DGGE banding profiles both for bacterial and fungal community weredigitized after average background subtraction for the entire gel.The relativeintensity of a specific band was transformed according to the sum of intensities of allbands in a pattern. Redundancy analysis (RDA) was conducted to determine therelationships between microbial community structure and physico-chemicalparameters by Canoco (version4.5). The results showed that approximate73.2%and75.5%of the variation in the bacterial and fungal species data were explained by allparameters. The temporal variation of bacterial community composition wassignificantly related to WSC (19.5%, P=0.002), ammonium (14.1%, P=0.004）andnitrate (8.5%, P=0.002), while the most variation in the distribution of fungalcommunity composition was statistically explained by pile temperature (17.0%,P=0.002), WSC (11.8%, P=0.002), and moisture content (8.5%, P=0.01). Thoseparameters were the most likely ones to influence, or be influenced by the bacterialand fungal species.
NH_3and its unincorporated form NH4+are the most important nitrogenouscompounds available in the compost materials. An alkaline pH during thecomposting process may lead to substantial loss of nitrogen as gaseous NH3. Theoxidation of ammonia is the first and rate-limiting step of nitrification, anddetermines the transformation balance between oxidized and reduced forms ofnitrogen. Both ammonia oxidizing bacteria (AOB) and archaea (AOA) employ thesame functional amoA gene, encoding a subunit of the ammonia monooxygenaseenzyme responsible for the first step of the nitrification process. The roles of AOAand AOB, and to what extent these ammonia oxidizers might affect nitrogentransformation balance during the composting process are not well understood yet.The aim of this study was to compare the relative contribution of AOA and AOB tonitrification during agricultural waste composting. Potential ammonia oxidation(PAO) rate was also determined. The amoA gene abundance and composition weredetermined using quantitative PCR (qPCR) and DGGE, respectively. Relationshipsbetween PAO rates and the amoA gene abundance were determined to assess thecontribution of AOA and AOB to nitrification.The results showed that the PAO ratevaried between29.3and89.9ng NO2-min-1g-1DW compost sample, with samplescollected on day2to day6displaying the highest activities. The PAO rate decreasedsignificantly during the thermophilic stage and increased further during thematuration stage and reached66.1ng NO2-min-1g-1DW compost sample by the endof the process. The archaeal amoA gene was abundant throughout the compostingprocess. Phylogenetic analyses of the archaeal amoA gene fragments for day4showed that all AOA sequences fell within the soil/sediment lineage. While thebacterial amoA gene abundance decreased to undetectable level during thethermophilic and cooling stages. The high temperature and low oxygenconcentration during the thermophilic and cooling stages might have provided anunfavourable condition for the AOB populations. Phylogenetic analyses of thebacterial amoA gene fragments for day50showed that most AOB sequences showinghigher sequence similarity to Nitrosomonas europaea/communis. DGGE showedmore diverse archaeal amoA gene composition when the PAO rate reached peak values. A significant positive relationship was observed between the PAO rate andthe archaeal amoA gene abundance (R2=0.554; P<0.001), indicating that archaeadominated ammonia oxidation during the thermophilic and cooling stages. Bacteriawere also related to ammonia oxidation activity (R2=0.503; P=0.03) especiallyduring the mesophilic and maturation stages.
As an important fraction of the total organic matter in the compost materials,the lignocellulose are resistant to biodegradation by microbial communities, addingadds difficulties to wastes disposal. Several species of basidiomycetes designated aswhite-rot fungi can efficiently decompose lignocellulose into carbon dioxide andwater in a variety of lignocellulosic materials. The inoculation with thoselignocellulolytic microorganisms has been widely used as a strategy that couldpotentially speed up the composting process and ultimately improve the quality ofcompost product. Phanerochaete chrysosporium (P. chrysosporium) has been widelyassumed one of the most active ligninolytic organisms among white-rot fungidescribed to date. Much attention has currently been drawn to the effects of P.chrysosporium inoculation on the sample maturity index, the enzyme activities andthe reduction of heavy metal toxicity. However, little information is available on theeffect of inoculation with P. chrysosporium on the indigenous microbialcommunities during agricultural waste composting. This research was conducted todistinguish between the separate effects of the P. chrysosporium inoculation andsample property heterogeneity induced by different inoculation regimes on theindigenous bacterial communities during agricultural waste composting. Fourseparate experiments, each in triplicate, were conducted in this experiment. Run Awas uninoculated with P. chrysosporium as control. Run B and Run C wereinoculated with1%of P. chrysosporium mycelium (fresh weight) during the firstfermentation phase (day2) and the second fermentation phase (day20), respectively.Run D was inoculated with the same amount of P. chrysosporium mycelium bothduring the first and the second fermentation phases. The bacterial communityabundance and structure were determined by the quantitative PCR and denaturinggradient gel electrophoresis analysis, respectively. Results showed that different inoculation regimes changed pile temperature, ammonium, nitrate, WSC, pH andC/N. The ratios of lignocellulose degradation for all runs reached final values ofabout50%,45%and40%for cellulose, hemicellulose and lignin, respectively.Statistically significant higher bacterial16S rDNA gene abundance was obtained intreatments with P. chrysosporium inoculation treatments, indicating a significantstimulatory effect of P. chrysosporium inoculation on the bacterial communityabundance. The bacterial community abundance significantly coincided with piletemperature, ammonium and nitrate (P<0.006). Variance partition analysis showedthat the P. chrysosporium inoculation directly explained20.5%(P=0.048) of thevariation in the bacterial communities, whereas the sample property changes inducedby different inoculation regimes indirectly explained up to35.1%(P=0.002). Thebacterial community structure was significantly related to pile temperature, WSCand C/N ratio when P. chrysosporium were inoculated. The C/N ratio solelyexplained7.9%(P=0.03) of the variation in community structure, whereas piletemperature, WSC explained7.7%(P=0.026) and7.5%(P=0.034), respectively. P.chrysosporium inoculation affected the indigenous bacterial communities mostprobably indirectly through increasing pile temperature, enhancing the substrateutilizability and changing other physico-chemical factors.
The fungal community structure and diversity were obtained by sequencingtechnology and the quantitative PCR (qPCR) method, respectively. By sequencing,956effective sequences in total were yielded for all20samples, which consisted of13unique OTUs at99%sequence identity. The dominant phylum across all pooledsamples was Ascomycota, specifically from the species Acremonium chrysogenum,Galactomyces geotrichum and Scytalidium thermophilum. Species of Coprinopsiscinerea and Mortierella angusta that affiliated with Basidiomycota and Fungiincertae sedis, respectively, were also extensively represented. Cladosporiumcladosporioides, Cryptococcus podzolicus, Debaryomyces nepalensis,Cystofilobasidium macerans, Eurotium amstelodami, Nigrospora oryzae, andPlectosphaerella cucumerina were present in samples collected during the earlystage (from day1to day7), but at low abundance. The white-rot fungi inoculants P. chrysosporium were present in relatively higher abundance in samples collectedduring the second fermentation phase (17.8-26.7%of total fungal communities). P.chrysosporium only accounted for4.4%of the total fungal population on day7forRun D. Principal component analysis based on relative OUT abundance indicatesthat the indigenous fungal communities might apparently not be changed by P.chrysosporium inoculants during the thermophilic stage (day4to day12, exceeding50°C). Indigenous fungal community structure significantly changed afterinoculation during the second fermentation phase (day13to day50). Samplesinoculated with P. chrysosporium during the second fermentation phase (i.e., Runs Cand D) contained higher proportion of A. chrysogenum and G. geotrichum affiliatedwith Ascomycota compared with the control (i.e., Run A) on Day50. Thosenon-inoculated samples (i.e., Runs A and B) that dominated by C. cinerea and S.thermophilum were well separated from those P. chrysosporium inoculated ones. Thetotal and indigenous fungal community abundances in samples with P.chrysosporium inoculation were statistically lower compared to the control (Run A)during the first7days. The regressions between fungal community abundance andsample properties showed that there were significant negative relationships betweenindigenous fungal18S rDNA gene abundance and C/N ratio (R2=0.4483, P<0.01)and WSC (R2=0.691, P<0.001), as well as a significant positive relationship betweenindigenous fungal18S rDNA gene abundance and moisture content (R2=0.2058,P=0.045). The results of redundancy analysis showed that the most variation indistribution of indigenous fungal community structure was statistically explained byC/N ratio (F=34.546, P=0.002), moisture content (F=3.471, P=0.032), and nitrateconcentration (F=5.219, P=0.012). Those factors as well as the interactions amongthem were the most likely ones to influence, or be influenced by the indigenousfungal communities in samples with different P. chrysosporium inoculation regimes.
氨是堆肥材料中主要的微生物可利用性含氮化合物，氮素的损失形式之一是氨的挥发。微生物将氨氧化为亚硝酸盐是硝化作用的限速步骤，决定着堆肥体系氮素得转移转化平衡。堆肥体系细菌和古细菌均具有编码氨单加氧酶的amoA功能基因，负责将氨转化为羟胺，完成堆肥体系氨的最终生物氧化。目前学界对氨氧化细菌和氨氧化古细菌在堆肥体系中的存在特征及在多大程度上影响堆肥体系氮素得转移转化平衡缺乏认识。本研究主要采用编码氨氧化菌的氨单加氧酶的amoA基因PCR-DGGE技术和荧光定量聚合酶链式反应（real-time PCR）技术，并结合堆肥基质的潜在硝化能力，比较农业废物堆肥过程中氨氧化古细菌和氨氧化细菌对堆肥基质硝化能力的贡献能力差异。结果显示，在每单位样品干重中，潜在硝化活性取值变化范围是29.3~89.9ng NO2-/(g min)。在堆肥2~6d内收集到的样品体现最高的硝化活性。随着高温期的到来，堆肥基质潜在硝化能力迅速降低，在腐熟期潜在硝化能力进一步增加，堆肥结束时达到66.1ng NO2-/(g min)。氨氧化古细菌和氨氧化细菌对堆肥理化参数的响应存在差异。古细菌amoA基因在整个堆肥进程中均有存在，主要来自于土壤/沉积物聚类（soil/sedimentcluster），这些物种与Candidatus Nitrososphaera gargensis等氨氧化古细菌有很近的遗传距离。而细菌的amoA基因仅在堆肥升温期和腐熟期检测到，全部属于亚硝化单孢菌属（Nitrosomonas），这些基因序列与欧洲亚硝化单孢菌（Nitrosomonas europaea）、Nitrosomonas communis/nitrosa等文献报道较多的已分离鉴定的亚硝化单孢菌发育关系最为接近。堆肥高温期和降温期过高的堆体温度和氨氮含量严重抑制了氨氧化细菌的种群活性。另外，氨氧化古细菌和细菌amoA基因DGGE图谱显示，古细菌amoA基因多样性在堆肥高温期达到最大值，而堆肥基质的潜在硝化能力同时达到峰值。潜在硝化能力PAO和古细菌amoA基因丰度之间存在显著正相关（R2=0.554， P<0.001），氨氧化古细菌对微生物氨氧化的功能主导作用主要发生在高温期和降温期。氨氧化细菌与堆肥基质潜在硝化活性同样显著正相关（R2=0.503，P=0.03），但这种对氮素转移转化的驱动作用主要体现在升温期和腐熟期。
木质纤维素因为结构复杂能够抵御微生物的生物降解作用，严重减缓了废物的堆肥化降解速度。大量研究表明，通过添加某些木质纤维素降解菌剂，可以有效地促进堆肥体系木质纤维素等难降解有机物的生物降解，提高堆肥效率并最终改善堆肥产品质量。黄孢原毛平革菌（Phanerochaete chrysosporium）是目前为止发现的降解木质素成分能力最强的一种白腐真菌（white-rot fungi）。近年来学者主要关注于P. chrysosporium接种对堆肥体系腐熟度指数、酶活、木质素降解速率和重金属毒性的钝化等影响。然而，我们对接种P. chrysosporium对农业废物堆肥化体系本土细菌和真菌种群的影响仍然知之甚少。采用不同阶段接种黄孢原毛平革菌（P. chrysosporium），设置4个堆肥体系，分别编号为Run A、Run B、Run C和Run D，每个体系设有3个平行。其中Run A作为没有接种P.chrysosporium的菌丝体的控制体系；Run B仅在堆肥的一次发酵阶段（2d）接种了1%的P. chrysosporium菌丝体（湿重/堆肥原料干重，下同）；Run C仅在二次发酵阶段（20d）接种了1%的P. chrysosporium菌丝体；Run D在一次发酵阶段和二次发酵阶段均接种1%的P. chrysosporium菌丝体。我们采用荧光定量PCR、克隆文库构建和PCR-DGGE等分子生物学技术研究不同P. chrysosporium的接种方式，及这些方式引起的基质异质性对农业废物堆肥体系本土细菌和真菌种群的影响。采用回归分析（regression analysis）、冗余分析（RDA）和方差分离（variance partition analysis）等多元分析方法计算和判定这些因素的影响大小及显著性。结果表明，不同P. chrysosporium接种方式显著改变了堆体基质的堆体温度、氨态氮、硝态氮、WSC、pH和C/N等参数；不同接种处理的堆体半纤维素、纤维素与木质素的降解率最终达到堆肥结束时的50%、45%和40%。在二次发酵阶段接种P. chrysosporium对木质素降解的促进作用更加明显。 P.chrysosporium接种对细菌种群丰度具有一定的刺激作用。一次发酵阶段和二次发酵阶段接种P. chrysosporium的堆体16S rDNA基因数量均显著高于未接种堆体。这也许说明，低分子量的有机物质被P. chrysosporium产生的各种胞外酶作用后释放到堆肥基质中，进而刺激了本土细菌种群的生长和代谢。细菌16S rDNA基因数量与堆体温度、铵态氮显著正相关，而与硝态氮显著负相关。不同P.chrysosporium接种策略下细菌种群组成与C/N、堆体温度和WSC显著相关。方差分离分析结果显示，它们分别解释了7.9%（P=0.03）、7.7%（P=0.026）和7.5%（P=0.034）的细菌种群组成。不同接种方式引起的堆肥基质条件变化（35.1%，P=0.002）对细菌群落的影响比接种本身（20.5%，P=0.048）更大。这些结果表明P. chrysosporium菌剂主要通过提高堆体温度、改善基质营养物质的可利用性和改变其他参数的方式来影响堆肥体系本土细菌群落的数量及组成。
克隆测序和系统发育树构建结果表明，20个堆肥样品共获得956个有效测序结果，分属于13种真菌物种。不同P. chrysosporium接种方式下的堆肥样品本土优势真菌为子囊菌门的产黄顶孢霉（Acremonium chrysogenum）、白地霉（Galactomyces geotrichum）和嗜热节格孢霉（Scytalidium thermophilum）等真菌。担子菌门的灰盖鬼伞（Coprinopsis cinerea）和未定地位真菌（Fungi incertaesedis）的奥古斯塔被孢霉（Mortierella angusta）在堆肥样品中也大量存在。枝状枝孢霉（Cladosporium cladosporioides）、隐球酵母菌（Cryptococcuspodzolicus）、 Cystofilobasidium macerans、德巴利酵母菌（Debaryomycesnepalensis）、阿姆斯特丹散囊菌（Eurotium amstelodami）、稻黑孢霉（Nigrosporaoryzae）与小不整球壳菌（Plectosphaerella cucumerina）数量较少，仅在堆肥初期存在（1d~7d）。一次发酵阶段未接种P. chrysosporium的堆体真菌丰度显著高于接种处理的堆体。在二次发酵阶段，真菌种群总数与本土真菌数逐渐降低，不同处理间没有显著差异。二次发酵阶段接种的外源白腐真菌P. chrysosporium能够比较顺利的完成在堆肥基质中的定殖与生长，其数量占总真菌总数的17.8~26.7%。堆肥初始样品本土真菌组成与后期样品差异明显，这一差异主要是由堆肥温度的变化所引起。二次发酵阶段接种显著改变了本土真菌种群组成。二次发酵阶段接种的堆体本土优势真菌物种主要为产黄顶孢霉（A. chrysogenum）和白地霉（G. geotrichum）；而未接种的堆体其本土优势真菌物种主要为枝状枝孢霉（C. cladosporioides）和嗜热节格孢霉（S. thermophilum）。回归分析显示本土真菌种群数量与C/N、WSC显著正相关，而与硝态氮显著负相关。冗余分析表明本土真菌种群的动态变化与C/N、含水率和硝态氮显著相关。 P.chrysosporium接种改变了堆肥基质的C/N、含水率和硝态氮等因素，进而影响本土真菌种群结构与丰度。
Bacteria and fungi species play significant roles in the decomposition andmineralization of agricultural organic wastes during composting. Their communitycompositions are likely influenced by several physico-chemical parameters incomposting systems. So far, the physico-chemical parameters have not beenevaluated simultaneously with the bacterial and fungal composition changes toseparate out their relative importance. It is of interest to conduct such research todetermine to what extent of differences in bacterial and fungal communities areinfluenced by these parameters, respectively. The goal of this study was to identifyand prioritize some of the physico-chemical parameters that contributed to bacterialand fungal community compositions during agricultural waste composting. Ricestraw, vegetables, soil and bran were homogenized at a ratio of11:3:8:2to simulateagrcultural wastes composting. Bacterial and fungal community compositions weredetermined by polymerase chain reaction-denaturing gradient gel electrophoresis(PCR-DGGE). DGGE banding profiles both for bacterial and fungal community weredigitized after average background subtraction for the entire gel.The relativeintensity of a specific band was transformed according to the sum of intensities of allbands in a pattern. Redundancy analysis (RDA) was conducted to determine therelationships between microbial community structure and physico-chemicalparameters by Canoco (version4.5). The results showed that approximate73.2%and75.5%of the variation in the bacterial and fungal species data were explained by allparameters. The temporal variation of bacterial community composition wassignificantly related to WSC (19.5%, P=0.002), ammonium (14.1%, P=0.004）andnitrate (8.5%, P=0.002), while the most variation in the distribution of fungalcommunity composition was statistically explained by pile temperature (17.0%,P=0.002), WSC (11.8%, P=0.002), and moisture content (8.5%, P=0.01). Thoseparameters were the most likely ones to influence, or be influenced by the bacterialand fungal species.
NH_3and its unincorporated form NH4+are the most important nitrogenouscompounds available in the compost materials. An alkaline pH during thecomposting process may lead to substantial loss of nitrogen as gaseous NH3. Theoxidation of ammonia is the first and rate-limiting step of nitrification, anddetermines the transformation balance between oxidized and reduced forms ofnitrogen. Both ammonia oxidizing bacteria (AOB) and archaea (AOA) employ thesame functional amoA gene, encoding a subunit of the ammonia monooxygenaseenzyme responsible for the first step of the nitrification process. The roles of AOAand AOB, and to what extent these ammonia oxidizers might affect nitrogentransformation balance during the composting process are not well understood yet.The aim of this study was to compare the relative contribution of AOA and AOB tonitrification during agricultural waste composting. Potential ammonia oxidation(PAO) rate was also determined. The amoA gene abundance and composition weredetermined using quantitative PCR (qPCR) and DGGE, respectively. Relationshipsbetween PAO rates and the amoA gene abundance were determined to assess thecontribution of AOA and AOB to nitrification.The results showed that the PAO ratevaried between29.3and89.9ng NO2-min-1g-1DW compost sample, with samplescollected on day2to day6displaying the highest activities. The PAO rate decreasedsignificantly during the thermophilic stage and increased further during thematuration stage and reached66.1ng NO2-min-1g-1DW compost sample by the endof the process. The archaeal amoA gene was abundant throughout the compostingprocess. Phylogenetic analyses of the archaeal amoA gene fragments for day4showed that all AOA sequences fell within the soil/sediment lineage. While thebacterial amoA gene abundance decreased to undetectable level during thethermophilic and cooling stages. The high temperature and low oxygenconcentration during the thermophilic and cooling stages might have provided anunfavourable condition for the AOB populations. Phylogenetic analyses of thebacterial amoA gene fragments for day50showed that most AOB sequences showinghigher sequence similarity to Nitrosomonas europaea/communis. DGGE showedmore diverse archaeal amoA gene composition when the PAO rate reached peak values. A significant positive relationship was observed between the PAO rate andthe archaeal amoA gene abundance (R2=0.554; P<0.001), indicating that archaeadominated ammonia oxidation during the thermophilic and cooling stages. Bacteriawere also related to ammonia oxidation activity (R2=0.503; P=0.03) especiallyduring the mesophilic and maturation stages.
As an important fraction of the total organic matter in the compost materials,the lignocellulose are resistant to biodegradation by microbial communities, addingadds difficulties to wastes disposal. Several species of basidiomycetes designated aswhite-rot fungi can efficiently decompose lignocellulose into carbon dioxide andwater in a variety of lignocellulosic materials. The inoculation with thoselignocellulolytic microorganisms has been widely used as a strategy that couldpotentially speed up the composting process and ultimately improve the quality ofcompost product. Phanerochaete chrysosporium (P. chrysosporium) has been widelyassumed one of the most active ligninolytic organisms among white-rot fungidescribed to date. Much attention has currently been drawn to the effects of P.chrysosporium inoculation on the sample maturity index, the enzyme activities andthe reduction of heavy metal toxicity. However, little information is available on theeffect of inoculation with P. chrysosporium on the indigenous microbialcommunities during agricultural waste composting. This research was conducted todistinguish between the separate effects of the P. chrysosporium inoculation andsample property heterogeneity induced by different inoculation regimes on theindigenous bacterial communities during agricultural waste composting. Fourseparate experiments, each in triplicate, were conducted in this experiment. Run Awas uninoculated with P. chrysosporium as control. Run B and Run C wereinoculated with1%of P. chrysosporium mycelium (fresh weight) during the firstfermentation phase (day2) and the second fermentation phase (day20), respectively.Run D was inoculated with the same amount of P. chrysosporium mycelium bothduring the first and the second fermentation phases. The bacterial communityabundance and structure were determined by the quantitative PCR and denaturinggradient gel electrophoresis analysis, respectively. Results showed that different inoculation regimes changed pile temperature, ammonium, nitrate, WSC, pH andC/N. The ratios of lignocellulose degradation for all runs reached final values ofabout50%,45%and40%for cellulose, hemicellulose and lignin, respectively.Statistically significant higher bacterial16S rDNA gene abundance was obtained intreatments with P. chrysosporium inoculation treatments, indicating a significantstimulatory effect of P. chrysosporium inoculation on the bacterial communityabundance. The bacterial community abundance significantly coincided with piletemperature, ammonium and nitrate (P<0.006). Variance partition analysis showedthat the P. chrysosporium inoculation directly explained20.5%(P=0.048) of thevariation in the bacterial communities, whereas the sample property changes inducedby different inoculation regimes indirectly explained up to35.1%(P=0.002). Thebacterial community structure was significantly related to pile temperature, WSCand C/N ratio when P. chrysosporium were inoculated. The C/N ratio solelyexplained7.9%(P=0.03) of the variation in community structure, whereas piletemperature, WSC explained7.7%(P=0.026) and7.5%(P=0.034), respectively. P.chrysosporium inoculation affected the indigenous bacterial communities mostprobably indirectly through increasing pile temperature, enhancing the substrateutilizability and changing other physico-chemical factors.
The fungal community structure and diversity were obtained by sequencingtechnology and the quantitative PCR (qPCR) method, respectively. By sequencing,956effective sequences in total were yielded for all20samples, which consisted of13unique OTUs at99%sequence identity. The dominant phylum across all pooledsamples was Ascomycota, specifically from the species Acremonium chrysogenum,Galactomyces geotrichum and Scytalidium thermophilum. Species of Coprinopsiscinerea and Mortierella angusta that affiliated with Basidiomycota and Fungiincertae sedis, respectively, were also extensively represented. Cladosporiumcladosporioides, Cryptococcus podzolicus, Debaryomyces nepalensis,Cystofilobasidium macerans, Eurotium amstelodami, Nigrospora oryzae, andPlectosphaerella cucumerina were present in samples collected during the earlystage (from day1to day7), but at low abundance. The white-rot fungi inoculants P. chrysosporium were present in relatively higher abundance in samples collectedduring the second fermentation phase (17.8-26.7%of total fungal communities). P.chrysosporium only accounted for4.4%of the total fungal population on day7forRun D. Principal component analysis based on relative OUT abundance indicatesthat the indigenous fungal communities might apparently not be changed by P.chrysosporium inoculants during the thermophilic stage (day4to day12, exceeding50°C). Indigenous fungal community structure significantly changed afterinoculation during the second fermentation phase (day13to day50). Samplesinoculated with P. chrysosporium during the second fermentation phase (i.e., Runs Cand D) contained higher proportion of A. chrysogenum and G. geotrichum affiliatedwith Ascomycota compared with the control (i.e., Run A) on Day50. Thosenon-inoculated samples (i.e., Runs A and B) that dominated by C. cinerea and S.thermophilum were well separated from those P. chrysosporium inoculated ones. Thetotal and indigenous fungal community abundances in samples with P.chrysosporium inoculation were statistically lower compared to the control (Run A)during the first7days. The regressions between fungal community abundance andsample properties showed that there were significant negative relationships betweenindigenous fungal18S rDNA gene abundance and C/N ratio (R2=0.4483, P<0.01)and WSC (R2=0.691, P<0.001), as well as a significant positive relationship betweenindigenous fungal18S rDNA gene abundance and moisture content (R2=0.2058,P=0.045). The results of redundancy analysis showed that the most variation indistribution of indigenous fungal community structure was statistically explained byC/N ratio (F=34.546, P=0.002), moisture content (F=3.471, P=0.032), and nitrateconcentration (F=5.219, P=0.012). Those factors as well as the interactions amongthem were the most likely ones to influence, or be influenced by the indigenousfungal communities in samples with different P. chrysosporium inoculation regimes.
引文
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