Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

Abstract

Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer ‘Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of ‘M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition–fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.

Abundance of planktonic methane-oxidizing bacteria in a subtropical reservoir

“…The probes DBACT-1027 and Mα450 perfectly match all 16S rRNA sequences of targeted MOB, detected in the clone libraries of the water from FTR (Kojima et al 2014). On the other hand, probes Mγ84 and Mγ705 have mismatches to some type I MOB detected in the FTR, and these MOB might have been missed with the probes.…”

“…In fact, predominance of the M. oxyfera -like MOB over proteobacterial MOB has hardly ever been reported, except for in cultures designed specifically to enrich them. In a previous study performed in a subtropical reservoir, high relative abundance of the M. oxyfera -like phylotype within the bacterial community was observed in the deep waters of a subtropical reservoir that was characterized by anoxic conditions (Kojima et al 2014). In the reservoir, Feitsui Reservoir (hereafter, FTR) in Taiwan, a close relative of M. oxyNote fera was the most frequently detected species-level phylotype among planktonic MOB detected using 16S rRNA gene sequences (Kojima et al 2014).…”

“…In a previous study performed in a subtropical reservoir, high relative abundance of the M. oxyfera -like phylotype within the bacterial community was observed in the deep waters of a subtropical reservoir that was characterized by anoxic conditions (Kojima et al 2014). In the reservoir, Feitsui Reservoir (hereafter, FTR) in Taiwan, a close relative of M. oxyNote fera was the most frequently detected species-level phylotype among planktonic MOB detected using 16S rRNA gene sequences (Kojima et al 2014). The reason for the dominance of this phylotype in the FTR is still unknown, but the unique MOB community in this reservoir provides an important opportunity to study the mechanisms determining community structure of MOB.…”

“…Its surface area is 10.2 km 2 , and it can store 406 10 6 m 3 of water, when the water surface elevation is at 170 m above sea level. During the current study period, the elevation of the water surface ranged from 158 to 169 m above sea level, and the water depth at the sampling point was around 100 m. Water samples were collected with a 5-liter Go-Flo bottle 130 (General Oceanics, Miami, FL, USA) at the same sampling point (121°34′E, 24°54′N) that was used in previous studies (Kojima et al 2014, Itoh et al 2015. The samples for catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) were taken from 6 depths (0, 10, 30, 50, 70, 90 m) during October 2012 to February 2014 and additional water samples were obtained from depths of 80 m and 100 m. The water samples were fixed with 2% (w/v) paraformaldehyde and were stored in a cooler box until filtration (within 6 hours).…”

Food web properties of the recently constructed, deep subtropical Fei-Tsui Reservoir in comparison with the ancient Lake Biwa

“…Long-term monitoring of methanotrophic food webs is of ecological importance in understanding how carbon cycling is altered in lakes affected by anthropogenic activities. In the FTR, it has been reported that MOBs dominate profundal bacterial communities, showing remarkable vertical and seasonal variations in community compositions (Kojima et al, 2014;Kobayashi et al, 2016). Itoh et al (2015) experimentally demonstrated that the methane oxidation activity is highest in deep sub-oxic layers, in which both dissolved methane and oxygen are available to MOBs.…”