Microbial community structure in a tropical Malaysian peat swamp forest: the influence of tree species and depth

Tropical peat swamp forests (TPSF) support enormous biodiversity and huge emergent trees despite their waterlogged, acidic and nutrient-depleted conditions. TPSF are presently subject to destruction and severe degradation due to drainage, logging, fire and agricultural conversion, however, the microbial ecology of these endangered ecosystem remains largely unknown. This study investigated the microbial diversity and composition in North Selangor peat swamp forest (NSPSF), Malaysia. Peat samples were obtained from three depths (surface, 45 cm and 90 cm) from around three common tree species in NSPSF – two emergent trees: Shorea uliginosa and Koompassia malaccensis (a nitrogen-fixing legume), and a palm Eleiodoxa conferta. Microbial diversity and composition were assessed through next-generation sequencing of 16S rRNA gene performed on Illumina MiSeq. Environmental parameters including water pH, dissolved oxygen, total nitrogen, total phosphorus, total phenolic contents and C/N ratio were found to be significantly different between depths, but not between tree species. The surface possessed the highest microbial diversity. Microbial diversity and composition were mainly influenced by the depth, but not the tree species, although tree species exhibited a small influence on the microbial composition at the surface and at 90 cm. Total nitrogen was found to be the core environmental parameter shaping the microbial composition in NSPSF. Proteobacteria was the dominant phylum, followed by Acidobacteria. The archaea displayed higher abundance with increasing depth, with Euryarchaeota as the most dominant phylum. Methanogenic archaea (class Thermoplasmata) were found more abundantly in deeper layers while methanotrophs (family Methylocystaceae) were more abundant at the surface. Rhodoplanes was the most abundant genus, and it is likely to be involved in nitrogen fixation. Ammonia-oxidizing archaea (AOA) were detected in the absence of ammonia-oxidizing bacteria (AOB), indicating that nitrification in TPSF is likely performed by AOA. The correlation analyses between the relative abundance of various phyla/classes/orders and environmental parameters revealed stronger impact of environmental parameters on the less-abundant microbial groups compared to the dominant lineages.

热带泥炭沼泽森林（Tropical peat swamp forests, TPSF）尽管处于积水、酸性且养分匮乏的环境中，仍孕育了极为丰富的生物多样性与超高大乔木。当前，TPSF因排水、采伐、火灾与农业开垦正遭受破坏与严重退化，但这一濒危生态系统的微生物生态学特征仍鲜为人知。本研究以马来西亚北雪兰莪泥炭沼泽森林（North Selangor peat swamp forest, NSPSF）为研究对象，探究了其中的微生物多样性与群落组成。研究人员从NSPSF内3种常见树木的周边区域采集了不同深度的泥炭样品，采样深度分为表层、45厘米与90厘米；3种树木包括2株超高大乔木：沼生娑罗双（Shorea uliginosa）与马来甘巴豆（Koompassia malaccensis，一种固氮豆科植物），以及1种棕榈植物Eleiodoxa conferta。研究采用Illumina MiSeq平台对16S rRNA基因进行高通量测序，以此解析微生物多样性与群落组成。研究发现，不同深度的环境参数（包括水体pH、溶解氧、总氮、总磷、总酚含量与碳氮比）存在显著差异，但不同树木物种间的环境参数并无显著区别。表层泥炭的微生物多样性最高。微生物多样性与群落组成主要受采样深度影响，而非树木物种；不过树木物种对表层与90厘米深度的微生物群落组成存在微弱影响。总氮是调控NSPSF内微生物群落组成的核心环境参数。变形菌门（Proteobacteria）是最优势的菌门，其次为酸杆菌门（Acidobacteria）。古菌的相对丰度随采样深度增加而升高，广古菌门（Euryarchaeota）为其最优势菌门。产甲烷古菌（Thermoplasmata纲）在更深的土层中丰度更高，而甲烷氧化菌（Methylocystaceae科）在表层泥炭中更为富集。红游动菌属（Rhodoplanes）为最优势菌属，其可能参与固氮过程。研究仅检测到氨氧化古菌（Ammonia-oxidizing archaea, AOA），未发现氨氧化细菌（Ammonia-oxidizing bacteria, AOB），这表明TPSF中的硝化作用大概率由AOA完成。对不同菌门、纲、目相对丰度与环境参数的相关性分析显示，相较于优势微生物类群，环境参数对低丰度微生物类群的影响更为显著。