Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments

Abstract

Background Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. Results Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50–100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0–50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. Conclusions This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

“…The vertical distribution of electron donors and acceptors showed an obvious impact on microbial functions, such as anaerobic oxidation of methane (AOM) and sulphate reduction [ 21 , 22 ]. Recently, we found that N 2 fixation rate increased while the diversity of diazotrophic communities decreased along the depth of mangrove sediments largely due to the vertical variation of salinity [ 23 ]. However, most of such studies were focused exclusively on the top 20 cm of mangrove sediments, which was considered as the layer with the greatest microbial diversity, biomass and activity [ 6 , 20 , 24 ].…”

Effects of Salinity on Assembly Characteristics and Function of Microbial Communities in the Phyllosphere and Rhizosphere of Salt-Tolerant Avicennia marina Mangrove Species

“…Mangrove ecosystems play an important role in biodiversity maintenance, wind protection, dike fixation, carbon storage, and seawater purification ( 2 ). Mangrove soil has a high salinity due to periodic tidal seawater immersion and intense biological salinization of mangroves ( 3 ). Mangrove plants have grown in this habitat for a long time and have specialized a set of adaptive mechanisms different from those of terrestrial or freshwater plants ( 4 ).…”

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter

“…Excess nitrate in the estuary results from runoff from terrestrial ecosystems and ultimately flows into the ocean . The neighboring mangrove and oceanic ecosystems have also been reported to harbor numerous heterotrophic ANR microbes even with a relatively low nitrate abundance. ,, To investigate their biogeography across the land–estuary–ocean continuum, we analyzed the taxonomic diversity of heterotrophic ANR bacteria in the mangrove, estuarine, and oceanic ecosystems. Through genomic assembly, we detected 8 out of 589 (mangrove), 38 out of 275 (estuarine), and 43 out of 957 (oceanic) MAGs containing both nasA and nirBD in the metagenomic datasets.…”