土壤微生物在维持生态系统服务方面发挥着重要作用(Wagg et al, 2014), 揭示城市绿地土壤微生物的多样性、生态学机制和功能对于城市绿地建设以及维持城市绿地可持续健康发展具有重要意义。同时, 土壤微生物是空气微生物的重要来源并可通过呼吸道进入人体。此外, 人的皮肤接触绿地土壤也会将土壤微生物引入人体, 从而影响人的身心健康(Delgado-Baquerizo et al, 2021; 任一等, 2021)。例如, 一些研究发现居住在农村和森林环境附近的居民比城市居民的皮肤细菌多样性更高(Hanski et al, 2012); 暴露于城市绿地可以增加皮肤和鼻腔微生物的多样性, 从而提高自身免疫力, 降低免疫代谢疾病的发生(Grönroos et al, 2019; Selway et al, 2020)。但是, 也有研究显示长时间户外暴露会增加感染性疾病发生的风险(Hanski et al, 2012)。因此, 城市绿地微生物对城市居民健康具有重要影响。城市森林公园是居民休闲活动的重要去处, 而其中的土壤微生物在生物地球化学循环过程中发挥重要作用(Falkowski et al, 2008; le Chatelier et al, 2013; Shade et al, 2013; Delgado-Baquerizo et al, 2021), 其多样性和群落构成是评估城市生态系统可持续发展的关键指标(Wei et al, 2016; Zhang et al, 2019), 是城市绿地生态系统健康的维持者(Ortiz et al, 2009), 对人类健康也具有重要的影响(Lin et al, 2022)。因此, 开展城市公园土壤微生物的群落研究具有重要的科学意义和实践价值。
阐明微生物群落构建的生态学过程(确定性和随机性)一直是生态学研究中的热点话题(Chase et al, 2010)。确定性过程涉及非随机性, 包括环境过滤, 与物种间适应度差异相关; 而随机过程主要反映物种相对多度的随机变化, 包括随机出生、死亡和扩散, 与物种间的适应度差异无关(Hubbell, 1979, 2001; Tilman, 2004)。近年来, 在研究人员对亚热带河流微型真核浮游生物(Chen et al, 2019)、温带草原土壤微生物(Liu et al, 2021)、农田土壤微生物(Xu et al, 2021)、不同的干旱生态系统(农田、森林、草地、湿地、沙漠) (Jiao et al, 2021)以及长江中下游水生植物芦苇(Phragmites australis)根系相关细菌(He et al, 2022)等研究发现, 确定性过程和随机性过程在微生物群落构建中发挥着重要作用。然而, 人们对城市公园细菌群落构建的生态学机制知之甚少, 相关研究亟待弥补。
包头市地处内蒙古高原的中西部半干旱地区。城市森林公园对调节城市气候具有重要作用, 是人们休闲的重要场所。本研究运用Illumina高通量测序技术对包头市3个较为典型的森林公园林下土壤细菌进行研究, 以探讨半干旱区城市公园林下土壤细菌的多样性、物种组成、群落构建机制以及潜在功能, 本研究可为城市绿地建设、生态功能的维持、人类健康等提供一定的科学依据。
1 材料与方法
1.1 样地选择及土壤采集
包头市地处内蒙古中西部地区, 年平均气温6.5℃, 年平均降水量为311.5 mm, 是典型的半干旱温带大陆性季风气候。本研究选取包头市奥林匹克公园(AL)、劳动公园(LD)和阿尔丁植物园(ZW) 3个较为典型的城市森林公园进行土壤样品的采集, 其中, 奥林匹克公园(2014年建设)地处包头市东部; 劳动公园(1958年建设)位于包头市中部; 阿尔丁植物园(2003年建设)位于包头市西部, 并且公园之间相隔约5 km。在LD和ZW公园内各设置10个10 m × 10 m样方, AL公园设置7个10 m × 10 m的样方(附录1)。依据五点取样法在每个样方去除表层凋落物后, 采集5份0-20 cm土壤并将其均匀混合为1份, 共获得27份混合土样。样品放入随身携带的冰盒以保持样品的新鲜度。运回实验室后, 每份土壤样品过2 mm筛去除土壤中的植物根系和石砂等杂质, 并分成2份, 1份(0.5 g)冻存于‒80℃冰箱用于后续土壤细菌的总基因组提取, 1份(10 g)在实验室内自然晾干用于土壤理化性质的检测, 本研究中检测的土壤性质包括土壤酸碱度pH、有效磷(AP)、速效钾(AK)、有效氮(AN), 测定方法参考杨剑虹等(2008)的方法进行。
1.2 土壤16S rDNA测序及生物信息学分析
土壤DNA提取完全按照DNeasy PowerSoil Pro Kit (250)试剂盒的说明书进行, 所提取的DNA用Nanodrop 2000检测浓度及质量并用0.8%的琼脂糖凝胶电泳检测其完整度。细菌选用16S V4-V5区通用引物515F (5'-GTGCCAGCMGCCGCGGTAA-3')和907R (5'-CCGTCAATTCMTTTRAGTTT-3')进行扩增, 每个样品扩增3个重复并合并。PCR产物纯化后测定浓度, 按照等摩尔混合均匀, 交由上海派森诺生物科技公司采用Illumina Noveseq PE250进行双端测序。
测序获得的原始数据, 首先使用cutadapt (v2.3)切除引物序列, 使用Vsearch (Rognes et al, 2016)的fastq_mergepairs命令进行序列的拼接, 并使用 fastq_filter命令对拼接后的序列进行质控后并去除低质量序列。接着使用Vsearch的derep_fulllength命令去除冗余序列, 并使用Usearch11 (Edgar et al, 2011)中的uchime2_ref命令检查嵌合体并去除, 进一步使用该软件中的cluster_otus命令划分OUT (operational taxonomic units), 最后使用Vsearch软件中的usearch_global命令依据 97%的相似性获得OTUs表。物种分类注释基于SILVA (138.1)数据库使用Vsearch中的sintax命令进行, 阈值设为0.65。对分类信息进行鉴定, 去除古菌、蓝细菌(叶绿体)和线粒体相关的OTUs。为了避免样品间测序深度差异对细菌的多样性和群落组成分析造成影响, 使用R v3.6.3中vegan包的rrarefy命令按照样品最小reads数(53,805)进行标准化处理。测序原始数据已上传至NCBI的SRA数据库(登录编号: PRJNA825285)。
1.3 统计分析
基于标准化后的数据均使用R v3.6.3 软件进行分析, 使用vegan包计算样品中细菌的alpha多样性; 基于Bray-Curtis相似性矩阵使用vegan包进行非度量多维尺度排序分析(non-metric multi-dimensional scaling, NMDS), 同时采用置换多元方差分析(PerMANOVA)检测细菌群落在不同公园间的差异显著性。使用冗余分析(redundancy analysis, RDA)分析土壤环境因子与细菌群落之间的关系, 同时使用rdacca.hp包评估环境因子对细菌群落差异的贡献大小(Lai et al, 2022)。此外, 为进一步研究城市公园林下土壤细菌的群落构建机制, 基于OTU多度数据使用中性群落模型(neutral community model, NCM)分析细菌OTU相对多度和频率间的关系, 以此检验中性过程对群落构建的影响(Sloan et al, 2006)。使用NST包的tNST函数, 基于OTU多度数据采用“bray”距离矩阵和“PF”零模型算法计算细菌群落的标准化随机率 (normalized stochasticity ratio, NST), 以此分析随机性过程和确定性过程对城市公园土壤细菌群落构建的作用(Ning et al, 2019)。同时, 为了增加NST分析结果的可靠性, 我们计算了“PF”零模型下基于“Jaccard”距离矩阵、“PP”零模型下基于“bray”和“Jaccard”距离矩阵的群落NST数值。使用iCAMP依据OTU的系统发育距离将细菌OTU划分为不同的bin, 并根据零模型计算每个bin的β-净关系指数(beta net relatedness index, βNRI)和Raup-Crick值(RC), 进一步量化各生态过程对群落构建的贡献。其中, βNRI > 1.96为异质选择(hetero- geneous selection, HeS); βNRI < - 1.96为同质化选择(homogeneous selection, HoS); |βNRI| ≤ 1.96且RC < - 0.95为均质扩散(homogenizing dispersal, HD); |βNRI| ≤ 1.96且RC > 0.95为扩散限制(dispersal limitation, DL); |βNRI| ≤ 1.96且|RC| ≤ 0.95为漂变(drift, DR) (Ning et al, 2020)。使用Tax4Fun程序(Aßhauer et al, 2015)对细菌OTU进行功能预测, 获得各个样品的KEGG Orthology (KO)的丰度并进行统计分析。
2 结果
2.1 城市公园土壤细菌的多样性
经过质控后, 从所有的2,504,993条原始序列中获得2,503,759条高质量的非嵌合体序列, 并将其划分为3,452个OTUs。基于SILVA (138.1)数据库进行物种注释, 经鉴定有3,391个OTUs属于细菌。按照所有样本中的最小reads数53,805标准化后, 有3,391个OTUs (reads数1,452,735)用于统计分析。
物种累积曲线分析结果表明, 3个研究区域的细菌OTU数随着样品数的增加已达到平台期, 意味着绝大多数的细菌OTUs被检测出来, 表明本研究能反映该城市公园土壤细菌的真实情况(图1a)。进一步分析发现, 该研究区域具有较高的物种丰富度, 其平均丰富度指数为2,388.81 ± 4.03 (mean ± SE)、平均Shannon多样性指数为9.16 ± 0.01 (mean ± SE)。3个城市公园间的物种丰富度存在一定的差异, LD公园丰富度最高(2,443 ± 9.37), 其次是ZW公园(2,392.90 ± 8.23), 而AL公园的丰富度最低(2,305.57 ± 17.48), 且LD公园与AL公园之间存在显著性差异(P < 0.05, 图1b)。
图1
图1
包头市三个森林公园土壤细菌多样性。(a)物种累积曲线; (b)丰富度指数。*表示Wilcoxon检验P < 0.05。AL: 奥林匹克公园; LD: 劳动公园; ZW: 阿尔丁植物园。
Fig. 1
Alpha diversity of soil bacteria in three forest parks in Baotou City. (a) Species accumulation curves; (b) Richness index, * indicates Wilcoxon test P < 0.05. AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.
2.2 城市公园土壤细菌的群落组成
图2
图2
土壤细菌群落前15个门和科水平的相对多度｡(a)门水平; (b)科水平｡AL: 奥林匹克公园; LD: 劳动公园; ZW: 阿尔丁植物园｡
Actinobacteriota: 放线菌门
Proteobacteria: 变形菌门
Acidobacteriota: 酸杆菌门
Chloroflexi: 绿弯菌门
Gemmatimonadota: 芽单胞菌门
Planctomycetota: 浮霉菌门
Myxococcota: 粘球菌门
Bcteroidota: 拟杆菌门
Armatimonadota: 装甲菌门
Firmicutes: 厚壁菌门
Entotheonellaeota: 肠杆菌门
Nitrospirota: 硝化螺旋菌门
Desulfobacterota: 脱硫杆菌门
Latescibacterota: 隐性菌门
Gemmatimonadaceae: 芽单胞菌科
Solirubrobacteraceae: 土壤红杆菌科Nitrosomonadaceae: 亚硝化单胞菌科
Geodermatophilaceae: 地嗜皮菌科
Comamonadaceae: 丛毛单胞菌科
Pseudonocardiaceae: 假诺卡氏菌科
Micromonosporaceae: 小单孢菌科
Xanthobacteraceae: 黄色杆菌科
Others: 其他类群
Fig. 2
Relative abundance of top 15 phyla and families of soil bacterial communities. (a) Phylum level, (b) Family level. AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.
NMDS排序分析发现3个公园的土壤细菌群落组成存在显著差异(stress = 0.12, P = 0.001), 其中, AL公园的土壤细菌群落明显区别于其他2个公园的土壤细菌群落(图3a)。此外, RDA分析表明, ZW和LD公园的土壤细菌群落与pH呈正相关, 而与AN、AP、AK呈负相关(图3b)。此外, pH、AN、AP和AK对细菌群落的总解释率为16.01%, 独立解释率分别为5.32%、2.55%、3.45%和4.69%, 表明环境因子是影响群落组成的重要因素(附录2)。为了探究各公园中多度显著差异的OTUs, LEfSe分析表明(LDA阈值为3), OTU_42、OTU_151、OTU_65等显著在AL公园中富集; OTU_316、OTU_82、OTU_31等显著在LD公园中富集; OTU_170、OTU_74、OTU_325等显著在ZW公园中富集(图4)。
图3
图3
包头市三个森林公园土壤细菌群落组成。(a)基于Bray-Curtis距离的细菌群落非度量多维尺度(NMDS)排序分析; (b)土壤细菌与土壤理化性状的冗余分析(RDA)。AP: 有效磷; AK: 速效钾; AN: 有效氮。AL: 奥林匹克公园; LD: 劳动公园; ZW: 阿尔丁植物园。
Fig. 3
Composition of soil bacterial communities in three forest parks in Baotou City. (a) Nonmetric multi-dimensional scaling (NMDS) analysis ranking analysis of bacterial communities based on Bray-Curtis distances. (b) Redundancy analysis (RDA) of soil bacteria and soil physicochemical. AP, Available phosphorus; AK, Available kalium; AN, Available nitrogen; AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.
图4
图4
基于可操纵分类单元(OTU)水平的土壤细菌群落差异(线性判别分析效应大小: LDA > 3, P < 0.05)。AL: 奥林匹克公园; LD: 劳动公园; ZW: 阿尔丁植物园。
Fig. 4
Differences in soil bacterial communities based on operational taxonomic units (OTUs) levels (linear discriminant analysis effect size: LDA > 3, P < 0.05). AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden.
2.3 城市公园土壤细菌生态组装过程
中性群落模型NCM分析发现在3个公园中均有较高的解释率, 其中, AL公园解释率最高(76.45%), 其次是LD公园(74.13%)和AL公园(62.44%) (图5a-c)。这说明随机过程在城市公园土壤细菌的群落组装中发挥重要作用。并且, ZW公园的迁移率(m = 0.8418)都高于其他两个公园(LD公园: m = 0.6993; AL公园: m = 0.4002), 表明ZW公园中的土壤细菌受扩散限制低于其他2个公园, 而AL公园受扩散限制的影响较大。NST分析结果显示, 3个公园的NST数值均大于50% (图5d)。 同时, 基于“PP”零模型、“Jaccard”距离矩阵的分析结果与上述NST分析结果一致(附录3), 这进一步说明随机性过程主导了城市公园细菌群落的构建。iCAMP进一步量化了该城市森林公园土壤细菌的生态过程, 3个公园的细菌群落构建是由漂变主导的, 分别为51.62%、63.55%、69.29%; 其次为同质化选择, 分别为25.83%、20.94%、23.24% (图6)。
图5
图5
土壤细菌群落的生态过程。(a)奥林匹克公园、(b)劳动公园和(c)阿尔丁植物园土壤细菌的中性群落模型(NCM); (d)三个公园的标准化随机率(NST)。
Fig. 5
Ecological processes in soil bacterial communities. Neutral community model (NCM) of soil bacteria in Olympic Park (a), Labor Park (c) and Aerding Botanical Garden (c); (d) The normalized stochasticity ratio (NST) in the three parks.
图6
图6
各生态过程对土壤细菌构建的重要性。基于零模型(iCAMP)表示生态过程的重要性, (a) AL: 奥林匹克公园; (b) LD劳动公园; (c) ZW: 阿尔丁植物园。HeS: 异质选择; HoS: 同质化选择; HD: 均质扩散; DL: 扩散限制; DR: 漂变。
Fig. 6
The relative importance of ecological processes in soil bacterial community assembly. The importance of ecological processes was indicated by infer community assembly mechanisms by phylogenetic-bin-based null model analysis (iCAMP), (a) AL, Olympic Park; (b) LD, Laodong Park; (c) ZW, Aerding Botanical Garden. HeS, Heterogeneous selection, HoS, Homogeneous selection, HD, Homogenizing dispersal, DL, Dispersal limitation, DR, Drift.
2.4 城市公园土壤细菌代谢功能预测
基于16S rRNA标记基因, 预测微生物群落的代谢功能。对主要的71个三级分类代谢途径功能(相对丰度 > 1.0%)进行了统计分析(图7)。71个主要代谢途径功能属于氨基酸代谢(amino acid metabolism)、萜类化合物和聚酮化合物的生物合成(biosynthesis of terpenoids and polyketides)、碳水化合物代谢(carbohydrate metabolism)等。22个二级分类水平, 其中膜运输、碳水化合物代谢、氨基酸代谢、能量代谢和信号转导是该城市公园林下土壤细菌主要的代谢途径。在二级分类水平中有16个在3个公园中差异显著(Kruskal-Wallis, P < 0.05)。例如, 碳水化合物代谢、核苷酸代谢在AL公园平均相对丰富度高于其他2个公园, 而在萜类化合物和聚酮化合物的生物合成中其他2个公园高于AL公园。
图7
图7
土壤细菌代谢功能差异。*表示Kruskal-Wallis P < 0.05。AL: 奥林匹克公园; LD: 劳动公园; ZW: 阿尔丁植物园。比例尺为代谢相对丰度的归一化值。
Fig.7
Differences in soil bacterial metabolic functions. * indicates Kruskal-Wallis P < 0.05. AL, Olympic Park; LD, Laodong Park; ZW, Aerding Botanical Garden. Scale bar is normalized value of metabolic relative abundance.
此外, 71个主要代谢途径功能中有38个在三组之间差异显著(Kruskal-Wallis, 0.01 < P < 0.05), 其中, ko00630乙醛酸和二羧酸代谢(glyoxylate and dicarboxylate metabolism)、ko00620丙酮酸代谢(pyruvate metabolism)、ko00051果糖和甘露糖代谢(fructose and mannose metabolism)、ko00650丁酸代谢(butanoate metabolism)、ko00730硫胺素代谢(thiamine metabolism)和ko00627氨基苯甲酸酯降解(aminobenzoate degradation)在3个公园之间差异极显著(P < 0.01), 这说明同一个城市的不同公园土壤细菌的功能存在显著差异。
3 讨论与结论
基于包头市3个公园林下土壤细菌的16S rRNA高通量测序统计分析发现, 包头市3个典型公园均表现出较高的细菌多样性, 建设较晚的AL公园林下土壤细菌多样性明显低于其他2个建设较早的公园, 这与张俊达(2019)研究的北京城市绿地中古典公园土壤细菌的多样性显著高于现代公园的结果相一致, 这意味着运营较长时间的公园生态系统更稳定, 具有更高的细菌多样性(Hui et al, 2017; 张骏达等, 2019)。本研究的城市林下土壤细菌群落以放线菌门、变形菌门、酸杆菌门、绿弯菌门和芽单胞菌门为优势菌门, 这与Zeng等(2019)的研究结果相一致, 但本研究中总计有35个细菌门被发现, 这说明包头城市公园林下土壤具有更丰富的细菌多样性(Lynd et al, 2002)。放线菌主要参与了木质素、纤维素等有机质分解的复杂过程, 同时具有很强的抗旱能力, 能产生刺激和促进植物生长的物质(Lynd et al, 2002; Stevenson et al, 2014; Zheng et al, 2017),这也是放线菌门在3个公园中均具有较高相对多度的原因。变形菌被认为是富营养化的细菌, 在含量较高的有效碳土壤中相对多度较高(Fierer et al, 2007), 这说明该市城市公园森林土壤有效碳含量可能较高, 但这需进一步验证。酸杆菌具有较强的抗逆性, 能够在寒冷的环境中生存, 包头市年均温度较低(6.5℃), 在这种条件下酸杆菌在纤维素降解中发挥重要作用(Pankratov et al, 2011)。绿弯菌门的细菌可以固定CO2并参与碳氮的循环(Xian et al, 2020)。由此可见, 这些优势细菌在城市绿地土壤物质循环过程中具有重要作用, 对于维持土壤健康具有重要意义。但是, 在科和属的水平上, 未确定分类的OTUs数分别占总OTUs数的37.54%和73.39%, 因此, 关于城市绿地中土壤微生物的研究仍然具有很大的空间。
基于OTU水平的LEfSe分析发现, 各公园中都有独特的生物标记物种(biomarker)。例如, OTU_42 (气微菌属 Aeromicrobium)、OTU_151 (沙壤土杆菌属Ramlibacter)、OTU_65 (链霉菌属Streptomyces)、OTU_114 (土壤红杆菌目Solirubrobacterales)、OTU_234 (丛毛单胞菌科Comamonadaceae)等显著在AL公园中富集, OTU_316 (Vicinamibacterales)、OTU_82 (土壤红杆菌目Solirubrobacterales)、OTU_31 (土微菌属Pedomicrobium)、OTU_97 (假诺卡氏菌属Pseudonocardia)、OTU_7 (γ-变形菌纲 Gammaproteobacteria)在LD公园中富集; OTU_170 (粘细菌门Myxococcota)、OTU_74 (红色杆菌属 Rubrobacter)、OTU_325 (Vicinamibacterales)、OTU_36 (克洛斯氏菌属Crossiella)、OTU_51 (Vicinamibacterales)在ZW公园中富集。这表明尽管3个公园空间距离不大, 但是都具有自己的指示性物种。而NMDS进一步分析发现3个公园的细菌群落组成存在显著差异。RDA显示这种差异是受到土壤环境因子pH、AN、AP和AK的影响, 这与前人在自然生境或城市生境中的研究结果相似(谭雪莲等, 2019; 任一等, 2021)。综上所述, 土壤中细菌类群的差异取决于采样地点以及相应土壤生境的影响(O’Brien et al, 2016)。
中性群落模型(NCM)分析发现, 该城市土壤细菌的中性群落模型拟合度较高(R2 > 60), 说明随机性过程在该城市森林公园土壤细菌群落的构建过程中发挥重要作用(Sloan et al, 2006; Bahram et al, 2016)。此外, 3个公园的m值存在差异, 例如AL公园R2值和m值相比其他2个公园都低, 表明该公园的细菌群落受扩散限制的影响较大, 而其他2个公园的细菌群落受扩散限制的影响较小。同时, 基于iCAMP分析显示, 与LD公园和ZW公园相比AL公园中的细菌群落受扩散限制的影响更大。我们推测这可能也与公园建成时间长短有关, 相较于LD公园和ZW公园年代较久远的公园, AL公园建成时间短, 公园内建筑结构如水泥路、园林栅栏等较新并维护较好, 阻碍微生物空间传播的能力较强, 因此导致其中细菌的扩散受到的限制更严重。iCAMP分析发现该城市森林土壤细菌群落主要是由随机过程中的漂变和确定性过程中的同质化选择驱动的, 这进一步论证了微生物群落的构建是由随机性过程和确定性过程共同决定的。但在不同的研究中各生态过程对微生物群落构建的重要性不同, 这主要与研究的具体生境和对象有关。非主要过程(漂变、弱选择、弱扩散、成种等)主导了公园林下土壤细菌群落的构建, 这与一些前人对微生物群落构建机制的研究结果相似(如: He et al, 2021; Sun et al, 2021), 但是如何把这些组分分解开, 量化它们的贡献大小, 目前仍然是一项挑战。此外, 本研究空间尺度较小, 每个公园中的人工管理模式相近(浇水、凋落物处理等), 且公园中的森林主要以当地的园林绿化树种河北杨(Populus hopeiensis)为主, 因此每个公园内的气候(温度、降水)可认为无差异, 同时每一个公园的林下环境如土壤性质, 凋落物成分等比较接近或相似, 所以导致同质化选择而非异质性选择驱动了细菌群落的构建。
土壤细菌是生物地球化学循环的重要参与者(Jenkins et al, 2017), 而基于高通量测序数据使用 Tax4Fun评估细菌群落潜在代谢功能已成为一种普遍被接受的方法(Wang et al, 2020)。本研究发现包头市3个城市公园林下土壤细菌功能均有较高的多样性, 其中膜运输、碳水化合物代谢、氨基酸代谢、能量代谢和信号转导是该城市公园林下土壤的主要代谢途径。但是, 主要代谢途径在3个地点间存在显著差异, 例如碳水化合物代谢、核苷酸代谢在AL公园的平均相对丰富度高于其他2个公园, 而在萜类化合物和聚酮化合物的生物合成中其他2个公园高于AL公园。同时三级代谢水平在公园之间也存在很大差异。这表明即使空间距离较小的城市公园间, 微生物的代谢功能也存在较大差异, 这与3个公园的微生物群落组成具有显著性差异这一结果一致。一项研究发现膜运输、碳水化合物代谢对重金属铀的污染生物吸收过程至关重要(Yan et al, 2016)。包头市是集冶金、稀土金属生产和机械制造为一体的综合性工业城市(Li et al, 2010; Si et al, 2015), 因此公园林下土壤可能存在一定程度的重金属污染。此外, 作为该城市工业污染排放的主要场地, 黄河存在大量的汞、铅和硒污染(Si et al, 2015)。但这些重金属如何影响土壤微生物及其代谢功能, 还需要我们进一步研究。
综上所述, 本研究发现包头市3个典型的城市公园林下土壤细菌具有较高的多样性, 运营时间越长的公园其多样性越高; 放线菌门、变形菌门、酸杆菌门和绿弯菌门是该城市公园林下土壤细菌的优势门, 并且不同的公园具有各自指示性微生物富集; 土壤细菌群落构建是由随机性过程和确定性过程共同决定, 但是随机性过程的作用强于确定性过程, 其中随机过程中的漂变和确定性过程中的同质化选择是群落构建的主要生态学过程; 发现膜运输、碳水化合物代谢、氨基酸代谢、能量代谢和信号转导是该城市公园林下土壤的主要代谢途径, 且不同公园之间的代谢功能存在较大差异。本研究可为城市绿地建设和修复提供一定的科学依据, 为人居环境的改善提供一定的指导。
附录 Supplementary Material
附录1 本研究采样地点与样方分布图
Appendix 1 The map of sampling sites and plots in present study
附录2 土壤因子对细菌群落组成的独立影响
Appendix 2 Independent effect of soil variables on bacterial community composition
附录3 不同距离矩阵和零模型方法下的标准化随机率(NST)
Appendix 3 Analysis of normalized stochasticity ratio (NST) based on different null models and distance matrices
参考文献
Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data
DOI:10.1093/bioinformatics/btv287 URL [本文引用: 1]
Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment
DOI:10.1038/ismej.2015.164 URL [本文引用: 1]
Stochastic community assembly causes higher biodiversity in more productive environments
DOI:10.1126/science.1187820 URL [本文引用: 1]
Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons
DOI:10.1186/s40168-018-0604-3 URL [本文引用: 1]
Global homogenization of the structure and function in the soil microbiome of urban greenspaces
DOI:10.1126/sciadv.abg5809 URL [本文引用: 2]
UCHIME improves sensitivity and speed of chimera detection
DOI:10.1093/bioinformatics/btr381 URL [本文引用: 1]
The microbial engines that drive Earth’s biogeochemical cycles
DOI:10.1126/science.1153213
PMID:18497287
[本文引用: 1]
Virtually all nonequilibrium electron transfers on Earth are driven by a set of nanobiological machines composed largely of multimeric protein complexes associated with a small number of prosthetic groups. These machines evolved exclusively in microbes early in our planet's history yet, despite their antiquity, are highly conserved. Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles. These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer. A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales.
Toward an ecological classification of soil bacteria
Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.
Short-term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota
DOI:10.1002/mbo3.645 URL [本文引用: 1]
Environmental biodiversity, human microbiota, and allergy are interrelated
Environmental biodiversity, human microbiota, and allergy are interrelated
Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs
DOI:10.1016/j.scitotenv.2021.145465 URL [本文引用: 1]
Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle-Lower Yangtze plain
DOI:10.1111/mec.16298 URL [本文引用: 1]
Tree dispersion, abundance, and diversity in a tropical dry forest
Patterns of tree abundance and dispersion in a tropical deciduous (dry) forest are summarized. The generalization that tropical trees have spaced adults did not hold. All species were either clumped or randomly dispersed, with rare species more clumped than common species. Breeding system was unrelated to species abundance or dispersion, but clumping was related to mode of seed dispersal. Juvenile densities decreased approximately exponentially away from adults. Rare species gave evidence of poor reproductive performance compared with their performance when common in nearby forests. Patterns of relative species abundance in the dry forest are compared with patterns in other forests, and are explained by a simple stochastic model based on random-walk immigration and extinction set in motion by periodic community disturbance.
Soil microbial communities are shaped by vegetation type and park age in cities under cold climate
DOI:10.1111/1462-2920.13660 URL [本文引用: 1]
Biochar alters the soil microbiome and soil function: Results of next-generation amplicon sequencing across Europe
DOI:10.1111/gcbb.12371 URL [本文引用: 1]
Stochastic community assembly decreases soil fungal richness in arid ecosystems
DOI:10.1111/mec.16047 URL [本文引用: 1]
Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package
DOI:10.1111/2041-210X.13800 URL [本文引用: 1]
Richness of human gut microbiome correlates with metabolic markers
DOI:10.1038/nature12506 URL [本文引用: 1]
Effects of the accumulation of the rare earth elements on soil macrofauna community
DOI:10.1016/S1002-0721(09)60233-7 URL [本文引用: 1]
Effect mechanism of land consolidation on soil bacterial community: A case study in Eastern China
DOI:10.3390/ijerph19020845 URL [本文引用: 1]
Relative importance of deterministic and stochastic processes on soil microbial community assembly in temperate grasslands
DOI:10.3390/microorganisms9091929 URL [本文引用: 1]
Microbial cellulose utilization: Fundamentals and biotechnology
DOI:10.1128/MMBR.66.3.506-577.2002
PMID:12209002
[本文引用: 2]
Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.
A general framework for quantitatively assessing ecological stochasticity
A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming
DOI:10.1038/s41467-019-13993-7 URL [本文引用: 1]
Spatial scale drives patterns in soil bacterial diversity
DOI:10.1111/1462-2920.13231 URL [本文引用: 1]
A study of air microbe levels in different areas of a hospital
DOI:10.1007/s00284-009-9398-7 URL [本文引用: 1]
Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat
DOI:10.1111/j.1462-2920.2011.02491.x
PMID:21564458
[本文引用: 1]
Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH.© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
Study on soil microbial diversity under five urban landscape plants
城市五种景观植物土壤微生物多样性研究
VSEARCH: A versatile open source tool for metagenomics
DOI:10.7717/peerj.2584 URL [本文引用: 1]
Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure
DOI:10.1016/j.envint.2020.106084 URL [本文引用: 1]
A meta-analysis of changes in bacterial and archaeal communities with time
DOI:10.1038/ismej.2013.54 URL [本文引用: 1]
Health risks of metals in contaminated farmland soils and spring wheat irrigated with Yellow River water in Baotou, China
DOI:10.1007/s00128-014-1435-y URL [本文引用: 2]
Quantifying the roles of immigration and chance in shaping prokaryote community structure
DOI:10.1111/j.1462-2920.2005.00956.x URL [本文引用: 2]
Water and temperature relations of soil Actinobacteria
DOI:10.1111/1758-2229.12199
PMID:25132485
[本文引用: 1]
Actinobacteria perform essential functions within soils, and are dependent on available water to do so. We determined the water-activity (aw ) limits for cell division of Streptomyces albidoflavus, Streptomyces rectiviolaceus, Micromonospora grisea and Micromonospora (JCM 3050) over a range of temperatures, using culture media supplemented with a biologically permissive solute (glycerol). Each species grew optimally at 0.998 aw (control; no added glycerol) and growth rates were near-optimal in the range 0.971-0.974 (1 M glycerol) at permissive temperatures. Each was capable of cell division at 0.916-0.924 aw (2 M glycerol), but only S. albidoflavus grew at 0.895 or 0.897 aw (3 M glycerol, at 30 and 37°C respectively). For S. albidoflavus, however, no growth occurred on media at ≤ 0.870 (4 M glycerol) during the 40-day assessment period, regardless of temperature, and a theoretical limit of 0.877 aw was derived by extrapolation of growth curves. This level of solute tolerance is high for non-halophilic bacteria, but is consistent with reported limits for the growth and metabolic activities of soil microbes. The limit, within the range 0.895-0.870 aw, is very much inferior to those for obligately halophilic bacteria and extremely halophilic or xerophilic fungi, and is inconsistent with earlier reports of cell division at 0.500 aw. These findings are discussed in relation to planetary protection policy for space exploration and the microbiology of arid soils. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.
Contribution of stochastic processes to the microbial community assembly on field- collected microplastics
DOI:10.1111/1462-2920.15713 URL [本文引用: 1]
Seasonal dynamics of soil microbial community structure in urban forest
城市森林土壤微生物群落结构的季节变化
Soil biodiversity and soil community composition determine ecosystem multifunctionality
Composition and diversity of soil microbial communities in the alpine wetland and alpine forest ecosystems on the Tibetan Plateau
DOI:10.1016/j.scitotenv.2020.141358 URL [本文引用: 1]
Amplicon-based metabarcoding reveals temporal response of soil microbial community to fumigation-derived products
DOI:10.1016/j.apsoil.2016.03.009 URL [本文引用: 1]
Research status and prospect on bacterial phylum Chloroflexi
绿弯菌的研究现状及展望
Microbial generalists and specialists differently contribute to the community diversity in farmland soils
Metagenomic analysis of microbial community in uranium-contaminated soil
DOI:10.1007/s00253-015-7003-5 URL [本文引用: 1]
Biogeography and the driving factors affecting forest soil bacteria in an arid area
DOI:10.1016/j.scitotenv.2019.04.184 URL [本文引用: 1]
Study of Soil Physicochemical Properties and Bacterial Community Structure of Urban Green Spaces in Beijing
北京市城区绿地土壤理化性质及细菌群落结构研究
Sustainability of urban soil management: Analysis of soil physicochemical properties and bacterial community structure under different green space types
DOI:10.3390/su11051395 URL [本文引用: 1]
Analysis of soil bacterial diversity in urban parks with different ages by high throughput sequencing
基于高通量测序技术的不同年代公园绿地土壤细菌多样性
A long-term hybrid poplar plantation on cropland reduces soil organic carbon mineralization and shifts microbial community abundance and composition
DOI:10.1016/j.apsoil.2016.11.017 URL [本文引用: 1]
