Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

Abstract

In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats.

Keywords: Archaea; Cyanobacteria; Lake Taihu; difference; macrophyte; sediment.

FIGURE 1

Location of sampling sites in two featured regions of Lake Taihu. Sites S1 to S6 denotes cyanobacteria-dominated zones and sites S7 to S11 denotes macrophyte-dominated zones.

FIGURE 2

(A) Non-metric multidimensional scaling ordination (NMDS) plot of the archaeal communities; (B) Redundancy analysis (RDA) of the archaeal community composition with sediment physichemical charateristics (blue arrows) for the 11 sampling sites. Samples in the cyanobacteria-dominated zone was marked by black filled cycles; Samples in the macrophyte-dominated zone was marked by red filled cycles; those physichemical charateristics which are significant correlation with the dynamics of archaeal were marked with ⋅ for 0.1 level, ^∗for 0.05 level and ^∗∗ for 0.01 level.

FIGURE 3

The overview of archaeal community composition at phylum level (CZ, cyanobacteria-dominated zone; MZ, macrophyte-dominated zone; Green shadow denoting the TACK supergroup; magenta denoting the DPANN supergroup; MHVG, Marine Hydrothermal Vent Group; MHVG-1, Marine Hydrothermal Vent Group 1; MEG, Miscellaneous Euryarchaeotic Group; those phyla with significant difference between the two regions were underlined with ^∗ for 0.05 level and ^∗∗ for 0.01 level).

FIGURE 4

Phylogenetic maximum-likelihood (ML) tree was built up for the total 605 representative Bathyarchaeota SSU rRNA gene sequences (black branches) obtained in the study with Terrestrial Hot Springs Crenarchaeotal Group as out-group. Sequences for typical Bathyarchaeota subgroups according to the nomenclatures promoted by Kubo et al. (2012) and Fillol et al. (2016) are used as major references for constructing the phylogenetic tree (red branches). Outer bar charts indicate the ratio of average sequence number belong to a certain OTU divided by the total number of sequences in a given sediment type. ML tree was built in ARB and edited with online tool iTOL (http://itol.embl.de/). CZ, cyanobacteria-dominated zone; MZ, macrophyte-dominated zone; subgroup name in black fonts indicates it contains bathyarchaeotal sequences generated in this study.

FIGURE 5

Comparison of specific phylum composition of sediment Archaea between cyanobacteria-dominated zone (CZ) and macrophyte-dominated zone (MZ): (A) phylum Euryarchaeota (SAGMEG, South African Gold Mine Euryarchaeotal Group); (B) methanogen at genus level (magenta shadow stands for order Methanobacteriales, green stands for order Methanomassiliicoccales, pink stands for order Methanosarcinales, cyan stands for order Methanomicrobiales, orange indicated order Methanococcales; Cd, Candidatus; Mme, Methanomicrobiaceae; Mbe, Methanobacteriaceae) (C) phylum Bathyarchaeota; (D) phylum Crenarchaeota (TMCG, Terrestrial Miscellaneous Crenarchaeotal Group); (E) phylum Thaumarchaeota (no order information is available, SCG, Soil Crenarchaeotic Group; MBGB, Marine Benthic Group B; MBGA, Marine Benthic Group A; MGI, Marine Group I). Archaeal lineages significantly different between the two regions were underlined with signs for significance: ^∗ for 0.05 level, ^∗∗ for 0.01 level and ^∗∗∗for 0.001 level.