Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers, denitrifiers, and anammox bacteria in sediments of estuarine tidal flats

Abstract

The spatial and temporal patterns of diversity, community structure, and their drivers are fundamental issues in microbial ecology. This study aimed to investigate the relative importance of spatial and seasonal controls on the distribution of nitrogen cycling microbes in sediments of estuarine tidal flats, and to test the hypothesis that metals impact the distribution of nitrogen-cycling microbes in the coastal system. Two layers of sediment samples were collected from three estuarine tidal flats of Laizhou Bay in 2010 winter and 2011 summer. The alpha diversities (Shannon and Simpson indices) and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA), denitrifier and anammox bacteria (AMB) were revealed using denaturing gradient gel electrophoresis and clone library analysis of amoA, nosZ and 16S rRNA gene markers. We found that both AOB and AMB exhibited distinct seasonal patterns in either alpha diversity or community turnover; AOA had different alpha diversities in two layers, but neither spatial nor seasonal patterns were found for their community turnover. However, no distinct spatiotemporal pattern was observed for either diversity or community composition of nosZ-type denitrifiers. For correlations between alpha diversities and environmental factors, significant correlations were found between AOB and ammonium, temperature and As, between denitrifiers and nitrite, salinity and Pb, and between AMB and Pb, ratio of organic carbon to nitrogen, ammonium, pH and dissolved oxygen. Salinity and sediment grain size were the most important factors shaping AOB and AOA communities, respectively; whereas AMB community structure was mostly determined by temperature, dissolved oxygen, pH and heavy metals As and Cd. These results stress that ammonia oxidizers, denitrifiers and anammox bacteria have generally different distributional patterns across time and space, and heavy metals might have contributed to their differentiated distributions in coastal sediments.

Spatiotemporal distributions and environmental drivers of diversity and community structure of nosZ-type denitrifiers and anammox bacteria in sediments of the Bohai Sea and North Yellow Sea, China

“…In the BS and NYS, algal blooms generally peak during May to July (Wei et al, 2004), and thus the organism is prevalent in that season. In contrast to other works (Magalhães et al, 2008;Mills et al, 2008;Fernandes et al, 2012;Yang et al, 2015;Yu et al, 2018), we observed that the Betaproteobacteriarelated nosZ group comprised a substantial fraction of the overall nosZ community detected in the Huanghe River estuary site. Betaproteobacteria is commonly detected in the freshwater and estuarine systems, such as Columbia River estuary (Crump et al, 1999), Changjiang River estuary (Feng et al, 2009), and Zhujiang (Pearl) River estuary (Liu et al, 2015).…”

“…The coastal sites, especially near the Huanghe River estuary, held higher diversity and distinct community structure of nosZ gene from central sites, probably because freshwater and sediment inputs from the river brought in terrigenous nosZ phylotypes, and on the other hand, some specifi c nosZ phylotypes could be evolved in the anthropogenic perturbation-dominated coastal setting. Similar to previous studies of coastal and marine nosZ -denitrifi ers (Magalhães et al, 2008;Mills et al, 2008;Fernandes et al, 2012;Yang et al, 2015;Yu et al, 2018), all nosZ sequences detected are related to proteobacteria, and Alphaproteobacteria formed the most dominant and ubiquitous putative nosZ group in the BS and NYS sediments, suggesting that this group was well adapted to coastal marine sediments and likely contributed importantly to nitrogen removal in the environments. Within Alphaproteobacteria, N .…”

“…Based on multiple analyses, salinity had the most signifi cant impact on nosZ -denitrifi er diversity, community structure, and distribution. Separation of nosZ genes according to salinity was also observed in estuarine sediments along a salinity gradient (Magalhães et al, 2008;Yang et al, 2015). Additionally, at the global scale, salinity was the major driver of nirS and nirK -denitrifi er communities in aquatic environments (Jones and Hallin, 2010).…”

“…The reduction of N 2 O to N 2 is catalyzed by nitrous oxide reductases (Nos), and this is an important step in the denitrifi cation process because greenhouse gas N 2 O is converted into N 2 and complete denitrifi cation is performed during this step (Zumft, 1997). Therefore, the nosZ gene is usually used as a biomarker to study the ecological behavior of denitrifying microorganisms in coastal environments (Scala and Kerkhof, 1999;Magalhães et al, 2008;Wyman et al, 2013;Wang et al, 2014;Yang et al, 2015).…”

Incorporation of Microbial Functional Traits in Biogeochemistry Models Provides Better Estimations of Benthic Denitrification and Anammox Rates in Coastal Oceans

“…The relative abundance of each T‐RF was calculated as the ratio of the peak area of that T‐RF to the total peak area of all of the T‐RFs detected for a given sample. Based on the T‐RFLP data, alpha diversity estimators (Shannon's index, H ; Simpson's index, 1/ D ; and evenness, E ) were calculated using an online diversity calculator (http://www.changbioscience.com/genetics/shannon.html; Yang et al, ).…”