Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
Front Microbiol. 2011 May 2;2:94. doi: 10.3389/fmicb.2011.00094. eCollection 2011.
Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
土壤是微生物多样性的巨大栖息地，其中存在着数千种共存的细菌、古菌和真菌物种。在广泛的空间尺度上，pH 值和土壤湿度等因素似乎决定了土壤细菌群落的多样性和结构。然而，在任何一个地点，细菌分类群的多样性都很高，而维持这种多样性的因素则尚未得到解决。候选因素包括有机底物的可用性和化学稳定性，并且由于它们似乎在门水平上构建细菌群落，我们研究了这些因素是否可能在更细的分类分辨率水平上构建细菌群落。通过 PhyloChip 微阵列分析核苷酸类似物标记 DNA 的 16S rRNA 基因组成，我们比较了 43 个门/纲中超过 2200 个细菌分类群对增加化学稳定性的有机底物的相对生长速率。随着易生物降解有机底物（即甘氨酸、蔗糖）的相对丰度增加的分类群数量众多（>500），系统发育聚类，主要发生在两个门（变形菌门和放线菌门）中，包括放线菌目、肠杆菌目、伯克霍尔德菌目、红环菌目、交替单胞菌目和假单胞菌目。随着更具化学稳定性的底物（即纤维素、木质素或单宁-蛋白质）的相对丰度增加的分类群数量较少（168），但系统发育分布更广，发生在八个门中，包括梭菌目、鞘氨醇单胞菌目、脱硫弧菌目。超过 6%的检测到的分类群，包括许多伯克霍尔德菌目，随着易生物降解和化学稳定性底物的相对丰度增加。响应分类群的中 rRNA 拷贝数中位数估计表明，这些模式与细菌生长策略广泛一致。总的来说，这些数据表明，内在易生物降解底物的可用性变化可能导致土壤细菌组成的可预测变化。
