Ubiquitous filter feeders shape open ocean microbial community structure and function.

The mechanism of mortality plays a large role in how microorganisms in the open ocean contribute to global energy and nutrient cycling. Salps are ubiquitous pelagic tunicates that are a well-known mortality source for large phototrophic microorganisms in coastal and high-latitude systems, but their impact on the immense populations of smaller prokaryotes in the tropical and subtropical open ocean gyres is not well quantified. We used robustly quantitative techniques to measure salp clearance and enrichment of specific microbial functional groups in the North Pacific Subtropical Gyre, one of the largest ecosystems on Earth. We discovered that salps are a previously unknown predator of the globally abundant nitrogen fixer Crocosphaera; thus, salps restrain new nitrogen delivery to the marine ecosystem. We show that the ocean's two numerically dominant cells, Prochlorococcus and SAR11, are not consumed by salps, which offers a new explanation for the dominance of small cells in open ocean systems. We also identified a double bonus for Prochlorococcus, wherein it not only escapes salp predation but the salps also remove one of its major mixotrophic predators, the prymnesiophyte Chrysochromulina. When we modeled the interaction between salp mesh and particles, we found that cell size alone could not account for these prey selection patterns. Instead, the results suggest that alternative mechanisms, such as surface property, shape, nutritional quality, or even prey behavior, determine which microbial cells are consumed by salps. Together, these results identify salps as a major factor in shaping the structure, function, and ecology of open ocean microbial communities.

Effects of ammonium and nitrite on growth and competitive fitness of cultivated methanotrophic bacteria.

The effects of nitrite and ammonium on cultivated methanotrophic bacteria were investigated. Methylomicrobium album ATCC 33003 outcompeted Methylocystis sp. strain ATCC 49242 in cultures with high nitrite levels, whereas cultures with high ammonium levels allowed Methylocystis sp. to compete more easily. M. album pure cultures and cocultures consumed nitrite and produced nitrous oxide, suggesting a connection between denitrification and nitrite tolerance.

Model of the molecular basis for hydroxylamine oxidation and nitrous oxide production in methanotrophic bacteria.

Many methane-oxidizing bacteria (MOB) have been shown to aerobically oxidize ammonia and hydroxylamine (NH(2)OH) to produce nitrite and nitrous oxide (N(2)O). Genome sequences of alphaproteobacterial, gammaproteobacterial, and verrucomicrobial methanotrophs revealed the presence of haoAB, cytL, cytS, nirS or nirK, and norCB genes that may be responsible for N(2)O production, and additional haoAB genes were sequenced from two strains of Methylomicrobium album. The haoAB genes of M. album ATCC 33003 were inducible by ammonia and NH(2)OH, similar to haoAB induction by ammonia in Methylococcus capsulatus Bath. Increased expression of genes encoding nitric oxide reductase (cNOR; norCB) was measured upon exposure of M. capsulatus Bath to NaNO(2) and NO-releasing sodium nitroprusside. Only incubations of M. capsulatus Bath with methane, ammonia, and nitrite produced N(2)O. The data suggest a possible pathway of nitrite reduction to NO by reversely operating NH(2)OH oxidoreductase and NO reduction to N(2)O by cNOR independently or in conjunction with ammonia-induced enzymes (i.e. HAO or cytochrome c'-ß). Results of this study show that MOB likely have diverse mechanisms for nitrogen oxide metabolism and detoxification of NH(2)OH that involve conventional and unconventional enzymes.

Ammonia cometabolism and product inhibition vary considerably among species of methanotrophic bacteria.

Ecological studies have indicated that relative abundances of Gammaproteobacteria methanotrophs (Gamma-MOB) vs. Alphaproteobacteria methanotrophs (Alpha-MOB) in nitrogen (N) impacted soils are dictated in part by their abilities to tolerate inhibitory effects of ammonium and nitrite. In particular, ammonia is a cometabolic substrate and competitive inhibitor of methane monooxygenase. The rates of ammonia and hydroxylamine oxidation and inhibition of methane-oxidizing activity by ammonium and nitrite were compared among two Gamma-MOB and two Alpha-MOB to determine whether methanotrophs of the same class shared similar physiological profiles. Each isolate exhibited unique K(m(app)) for ammonia and V(max) for nitrite production with or without reductant (methane or sodium formate). The rates of nitrite production from hydroxylamine followed similar trends to rates of ammonia oxidation, indicating that hydroxylamine-oxidizing enzymes were central participants in the ammonia-oxidizing pathway. Methylomonas methanica was incapable of either ammonia or hydroxylamine oxidation. A broad range of sensitivities to ammonium and nitrite inhibition were measured with little consistency between isolates of the same class. The results indicate that physiological responses, and perhaps environmental adaptations, to N compounds are organism specific for methanotrophs.