Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

Abstract

Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.

Mimicking microbial interactions under nitrate‐reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio

“…That genome harbored the metabolic potential for some fermentative pathways, hydrogen production or consumption and dissimilatory sulfate reduction. Interestingly, a recent amplicon sequencing survey of river sediments impacted by freshwater mussels discovered the co-occurrence of anammox bacteria, nitrate-and nitritedependent methanotrophs as well as Thermodesulfovibriolike sequences (Black et al, 2017). Their survey did not target sulfide-dependent denitrifiers, but proteobacteria were abundantly present and could potentially be involved in nitrate-dependent sulfide oxidation.…”

Peer Review #3 of "Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management (v0.2)"

“…Mussels are known ecosystem engineers that can substantially modify their habitats through biological processes such as sediment filtration and biodeposition of fecal matters (Bril et al 2014). The presence of mussels has been reported to cause to a 4-fold decrease in the relative abundance of Plantomycetes in a freshwater system in Mississippi, USA (Black et al 2017). Manuscript to be reviewed growth promoting and inhibiting effects to its host and other algal species, respectively (Bowman 2006).…”

Metagenomic analysis of nitrogen‐cycling genes in upper Mississippi river sediment with mussel assemblages

“…The most distinct nitrification genes were most closely related to NOB Nitrospira and comammox Nitrospira. It is not surprising that Nitrospira species dominated the nitrification biomarkers due to their metabolic diversity (Koch et al, 2015;Lücker et al, 2010), domination within freshwater sediments (Altmann, Stief, Amann, de Beer, & Schramm, 2003), increased abundance in sediments with mussels (Black et al, 2017;Zheng, Tang, Zhang, Qin, & Wang, 2017), and greater abundance from invertebrate bioturbation activities (Shen et al, 2017). Finding amoA biomarkers from comammox Nitrospira clades suggests that the presence of mussels may enhance the genetic potential for complete nitrification.…”

“…In a previous study, we showed that sediment underlying a native freshwater mussel assemblage harbored microbial communities with lower species richness and evenness as compared to mussel-free sediment (Black, Chimenti, & Just, 2017). Additionally, mussels had a distinct and significant effect on the vertical distribution of multiple N-cycling microorganisms, including NO − 2 oxidizing bacteria (NOB) in the genus Nitrospira, aerobic NH 3 oxidizing bacteria (AOB) in family Nitrosomonadaceae, and anammox bacteria from candidate genus Brocadia.…”