Ammonia‐oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

Abstract

The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2's largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean.

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

“…This observation confirms previous studies that find that the dominant AOB in estuarine and marine environments appear to fall within divergent evolutionary clades (McCaig et al, 1994;Freitag and Prosser, 2004;Ward et al, 2007;Mosier and Francis, 2008). So far, there are no cultured isolates from this group, although Mosier and Francis, (2008) found sequences in an enrichment culture from the San Francisco Bay estuary.…”

Microbial community composition in sediments resists perturbation by nutrient enrichment

“…We used the RFR from the functional gene microarray (Ward et al, 2007;Bulow et al, 2008) to quantify the relative contribution of each archetype to the total nirS signal and determine the distribution of nirS-containing phylotypes in both the PIE and GSM marshes. The RFR for the 39 archetypes found in both marshes was remarkably consistent, with only minor differences as a result of fertilization in the GSM experiment, and no differences as a result of fertilization in the PIE experiment (Figure 4).…”

“…After amplification, PCR products were pooled and purified with the QIAquick PCR purification kit (Qiagen). PCR products were then labeled using the Klenow enzyme and hybridized to the array following standard methods (Ward et al, 2007;Bulow et al, 2008). After hybridization, the slides were washed (Ward et al, 2007) and scanned on an Agilent Laser Scanner (Agilent Technologies, Palo Alto, CA, USA).…”

“…Each slide contains eight arrays and each array consists of four replicate blocks. Data were quality checked (Ward et al, 2007;Bulow et al, 2008) and then the fluorescence from the Cy3-bound nirS sequences were compared with the Cy5 fluorescence to determine the fluorescence ratio for each probe after background fluorescence was subtracted. The Cy3/Cy5 ratios were first normalized for variations in fluorescence intensities across the slide by comparing Cy3/Cy5 fluorescence from internal standards within each array.…”

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment

“…Molecular approaches, such as functional gene arrays, facilitate a relatively easy assessment of the information in the microbenthic community, including community structure and function (Lu et al, 2012). Various studies have demonstrated the capacity of functional gene arrays to detect microbial community responses to environmental stressors Liu et al, 2010;Wang et al, 2009;Ward et al, 2007;Wu et al, 2008;Yergeau et al, 2007;Zhou, 2003), including heavily contaminated habitats (Lu et al, 2012;Neufeld et al, 2006;Van Nostrand et al, 2009;Xie et al, 2011). The results of these studies and other approaches evaluating the response of bacterial communities on environmental perturbation (chemically or physically) have demonstrated changes in the respective community structure and function (dos Santos et al, 2011;Findlay et al, 1990;Suarez-Suarez et al, 2011), thereby forming the basis for our hypothesis.…”