Metabolic strategies of free-living and aggregate-associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone

Abstract

The Black Sea is a permanently anoxic basin with a well-defined redox gradient. We combine environmental 16S rRNA gene data from clone libraries, terminal restriction fragment length polymorphisms, and V6 hypervariable region pyrosequences to provide the most detailed bacterial survey to date. Furthermore, this data set is informed by comprehensive geochemical data; using this combination of information, we put forward testable hypotheses regarding possible metabolisms of uncultured bacteria from the Black Sea's suboxic zone (microaerophily, nitrate reduction, manganese cycling, and oxidation of methane, ammonium, and sulfide). Dominant bacteria in the upper suboxic zone included members of the SAR11, SAR324, and Microthrix groups and in the deep suboxic zone included members of BS-GSO-2, Marine Group A, and SUP05. A particulate fraction (30 μm filter) was used to distinguish between free-living and aggregate-attached communities in the suboxic zone. The particulate fraction contained greater diversity of V6 tag sequences than the bulk water samples. Lentisphaera, Epsilonproteobacteria, WS3, Planctomycetes, and Deltaproteobacteria were enriched in the particulate fraction, whereas SAR11 relatives dominated the free-living fraction. On the basis of the bacterial assemblages and simple modeling, we find that in suboxic waters, the interior of sinking aggregates potentially support manganese reduction, sulfate reduction, and sulfur oxidation.

Oxidation kinetics and inverse isotope effect of marine nitrite-oxidizing isolates

“…comm.). The use of such a lower isotope effect may be appropriate because other OMZ regions (like the eastern tropical North Pacific off Costa Rica OMZ, the Namibian OMZ, the Black Sea OMZ, and the Baltic Sea; Labrenz et al 2007, Fuchsman et al 2011, Füssel et al 2012, Spieck et al 2014, Buchwald et al 2015) host predominantly Nitrospina, for which we find a low isotope effect in this study. This shows that a more accurate assessment of isotope effects and the kinetic parameters that determine these effects is urgently needed to better constrain biogeochemical models.…”

Water column biogeochemistry of oxygen minimum zones in the eastern tropical North Atlantic and eastern tropical South Pacific oceans

“…These aggregates, more commonly known as marine snow, contain microscale redoxclines under anoxic conditions (Alldredge and Cohen, 1987;Karl and Tilbrook, 1994;Woebken et al, 2007). Moreover, aggregate communities appear to be distinct from bulk water collected samples (Fuchsman et al, 2011). These communities were suggested to have active manganese reduction, sulfate reduction and sulfide oxidation at the interior of the aggregates.…”

Microbial Surface Colonization and Biofilm Development in Marine Environments

“…In non-and less-eutrophic marine environments such as pristine estuaries and offshore waters, where the majority of the particles are biogenic and thus organically enriched (123), significantly different community structures of particle-associated and free-living microorganisms are commonly found (108,114,(127)(128)(129). Particle-associated bacterial communities are frequently enriched in the marine Roseobacter clade (MRC) bacteria of the Alphaproteobacteria; the Alteromonadaceae and Vibrionaceae groups of the Gammaproteobacteria; as well as the Deltaproteobacteria, Bacteroidetes, and Planctomycetes (108,127,(130)(131)(132)(133)(134)(135)(136)(137). Many of these bacteria produce extracellular enzymes for biopolymer degradation, and some require suboxic or anoxic microniches within particles to support microaerophilic or anaerobic metabolism.…”

“…For example, in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, particles contribute 100% of the activity reducing nitrate to nitrite and 53 to 85% of N 2 production by denitrification and anammox (167). P cycling processes such as eDNA secretion (168,169) and particulate organic phosphorus degradation (153,170,171) are enhanced on marine particles, as are microbial S cycling activities such as sulfate reduction (133,141,147,153,172), sulfur oxidation (133,(146)(147)(148)153), and organic S compound (e.g., the algal osmolyte dimethylsulfoniopropionate [DMSP]) transformation and degradation (153,(173)(174)(175). As noted above, surface-and particle-associated microorganisms also contribute substantially to marine iron cycling processes, such as iron oxidation and reduction (78, 147, 176-178), siderophore-mediated iron solubilization and uptake (153,(179)(180)(181), iron transport among different oceanic environments (182), and biocorrosion (18, 69, 72, 81).…”