Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea

Abstract

A culture-independent examination of microbial diversity in mobile deltaic sediments from the Gulf of Papua, Papua New Guinea, was conducted by sequence analysis of 16S rDNA clone library. Universal small subunit primers were used to amplify DNA extracted from the sediment. Of 91 clones randomly selected from the library, 33 contained unique non-chimeric sequences. Analysis of these unique sequences showed that the majority of them belonged to bacteria (94.5%), with proteobacteria being the dominant division (74.8%). One sequence belonging to Crenarchaeota and another to Euryarchaeota were found as well. Bacterial sequences belonging to the following major divisions were identified: Cytophaga-Flexibacter-Bacteroides (5.5%), low GC Gram-positives (1.1%), Nitrospira group (3.3%), OP8 candidate division (2.2%), OS-K candidate division (2.2%), Planctomyces (1.1%), alpha, delta, gamma and epsilon-subdivisions of Proteobacteria (4.4, 20.9, 19.8 and 23.1%, respectively) and Spirochaetales (4.4%). The composition of 16S rDNA library of the Gulf of Papua sediments is similar to those for deepwater sediments from around the Japanese Islands, indicating a possible cosmopolitan nature of microbial communities in suboxic and anoxic sediments of the Pacific. It appears that many Papua/New Guinea sequences are loosely affiliated with bacteria involved in sulfur cycling, thus supporting the hypothesis that the sulfur cycle may be important in early diagenesis of suboxic sediments.

Molecular characterization of microbial community in nitrate-removing activated sludge

“…Zumft and other researchers reported that ammoniaoxidation should sustain nitrate-reduction [2,28,29,32]. Ammonia-oxidizing and nitrite-oxidizing bacteria have been detected in other anoxic environments by the culturing method (MPN) [26] and nitrite-oxidizing bacteria have been detected in anoxic sediments of the Paci¢c by sequence analysis of the 16S rRNA clone library [27]. We also found that nitrifying bacteria inhabited two reactors operated under anoxic conditions using culturing and nonculturing methods.…”

High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: identification of two new bacterial candidate divisions

“…The Kourou^Sinnamary site in French Guiana shares some similar biogeochemical characteristics with tropical Gulf of Papua mobile muds [18], which may help to explain similarities in clone libraries. Although French Guiana and Gulf of Papua libraries do not share closely related low-level taxonomic sequences, the major phylogenetic and physiological groups of bacteria present in these libraries are similar.…”

“…KS43f is likely to originate from a sulfate-reducing bacterium, a large number of Q-proteobacterial 16S rDNA sequences (KS25f, KS30, KS38, KS45f, KS72, KS75, KS86, KS90) may have come from potential aerobic sul¢de oxidizers, and several K-proteobacterial sequences (KS12, KS14, KS24) are related to sul¢te oxidizers. The lack in the French Guiana library of 16S rDNA sequences from anaerobic sul¢de-oxidizing O-proteobacteria, found in the Gulf of Papua [18] and Japanese Island sediments [20^22], is noteworthy. The major di¡erence in sulfur cycle reactions in the two mobile mud environments appears to be that oxidation of sulfur species in French Guiana muds is mainly aerobic, whereas both aerobic and anaerobic sul¢de oxidizers are present in the Gulf of Papua muds.…”

“…Sedimentary biogeochemical reactions are dominated by iron rather than sulfate reduction, although modest rates of sulfate reduction have been detected [1,17]. Molecular analysis of prokaryotic communities in Gulf of Papua mobile muds [18] indicated that many Papua New Guinea sequences were loosely a¤liated with bacteria involved in sulfur cycling, supporting a hypothesis that a sulfur cycle intermediate between C and Fe, Mn-oxides may be important in the early diagenesis of suboxic sediments. Additional support for serial redox coupling between C and S^Fe comes from the fact that sequences in the 16S rDNA Gulf of Papua sediment library were similar to those for deepwater sul¢dogenic sediment from around the Japanese Islands [19^22].…”

Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands

“…Bacteria within coastal and shelf sediments play an important role in global biogeochemical cycles, as they are the ultimate sink of most terrestrially derived compounds and a high proportion of marine particle flux. Despite a growing understanding of the global biogeochemical importance of these sediment habitats (Berelson et al, 1990;Blackburn and Blackburn, 1993;Vanduyl et al, 1993;Codispoti et al, 2001), little is known of the bacterial communities inhabiting them (Cifuentes et al, 2000;Todorov et al, 2000;Madrid et al, 2001;Kim et al, 2004), nor the factors influencing their distribution (Bowman et al, 2005;Polymenakou et al, 2005). Marine microbial diversity in the ocean has been the subject of intense recent study (Giovannoni et al, 1990;Fuhrman and Ouverney, 1998;Giovannoni and Rappe, 2000;Venter et al, 2004).…”