The Osmolyte Ties That Bind: Genomic Insights Into Synthesis and Breakdown of Organic Osmolytes in Marine Microbes

The production and consumption of organic matter by marine organisms plays a central role in the marine carbon cycle. Labile organic compounds (metabolites) are the major currency of energetic demands and organismal interaction, but these compounds remain elusive because of their rapid turnover and concomitant minuscule concentrations in the dissolved organic matter pool. Organic osmolytes are a group of small metabolites synthesized at high intracellular concentrations (mM) to regulate cellular osmolarity and have the potential to be released as abundant dissolved substrates. Osmolytes may represent an essential currency of exchange among heterotrophic prokaryotes and primary and secondary producers in marine food webs. For example, the well-known metabolite dimethylsulfoniopropionate (DMSP) is used as an osmolyte by some phytoplankton and can be subsequently metabolized by 60% of the marine bacterial community, supplying up to 13% of the bacterial carbon demand and 100% of the bacterial sulfur demand. While marine osmolytes have been studied for decades, our understanding of their cycling and significance within microbial communities is still far from comprehensive. Here, we surveyed the genes responsible for synthesis, breakdown, and transport of 14 key osmolytes. We systematically searched for these genes across marine bacterial genomes (n = 897) and protistan transcriptomes (n = 652) using homologous protein profiles to investigate the potential for osmolyte metabolisms. Using the pattern of gene presence and absence, we infer the metabolic potential of surveyed microbes to interact with each osmolyte. Specifically, we identify: (1) complete pathways for osmolyte synthesis in both prokaryotic and eukaryotic marine microbes, (2) microbes capable of transporting osmolytes but lacking complete synthesis and/or breakdown pathways, and (3) osmolytes whose synthesis and/or breakdown appears to be specialized and is limited to a subset of organisms. The analysis clearly demonstrates that the marine microbial loop has the genetic potential to actively recycle osmolytes and that this abundant group of small metabolites may function as a significant source of nutrients through exchange among diverse microbial groups that significantly contribute to the cycling of labile carbon.

Dependence of an aquatic insect population on contemporaneous primary production

Characterizing the dynamics of energy flow through ecosystems requires quantifying the degree to which primary and secondary production are coupled. This coupling is expected to be tight in ecosystems with high internal production relative to external carbon and energy inputs. We experimentally quantified the dependence of aquatic insect emergence on fresh primary production, specifically for the midge population in Lake Myvatn, Iceland. Using field mesocosms, we manipulated algal primary production by reducing light availability via shading. We then used dissolved oxygen incubations to estimate fluxes of carbon through photosynthesis (i.e., gross primary production or "GPP") over the course of the experiment. We found that elevated GPP was associated with higher emergence rates of adults, as judged both by comparison of emergence across the experimental shading treatments and estimates of in situ GPP within the mesocosms. Furthermore, larger adults emerged earlier than smaller ones, suggesting that asymmetries in resource availability among individuals affected the timing of emergence. Nonetheless, midge emergence was substantial under light-limiting conditions, indicating that while midges benefit from primary production contemporaneous with larval development, they are also capable of completing their life cycles on carbon already existing in the organic matter pool. Our results show that even in systems with limited allochthonous inputs, contemporaneous primary production may be not necessary for high secondary production and insect emergence. Instead, consumers can develop from consumption of biomass derived from past autochthonous primary production. This suggests that primary production and consumer dynamics can be partially decoupled in time in systems that depend on internal production.

Potential greenhouse gas production by organic matter decomposition in thawing subsea permafrost

<p>Subsea permafrost extends over vast areas across the East Siberian Arctic Ocean shelves and might harbor a large and vulnerable organic matter pool. Field campaigns have observed strongly elevated concentrations of CH<sub>4</sub> in seawater above subsea permafrost that might stem from microbial degradation of thawing subsea permafrost organic matter, from release of CH<sub>4</sub> stored within subsea permafrost, from shallow CH<sub>4</sub> hydrates or from deeper thermogenic/petrogenic CH<sub>4</sub> pools. We here assess the potential production of CH<sub>4</sub>, as well as CO<sub>2</sub> and N<sub>2</sub>O by organic matter degradation in subsea permafrost after thaw. To that end, we employ a set of subsea permafrost drill cores from the Buor-Khaya Bay in the south-eastern Laptev Sea where previous studies have observed a rapid deepening of the ice-bonded permafrost table. Preliminary data from an ongoing laboratory incubation experiment suggest the production of both CH<sub>4</sub> and CO<sub>2</sub> by decomposition of thawed subsea permafrost organic matter, while N<sub>2</sub>O production was negligible. These data will be combined with detailed biomarker analysis to constrain the vulnerability of subsea permafrost organic matter to degradation to greenhouse gases upon thaw.</p>

Impact of soil use on aggregate stability and its relationship with soil organic carbon at two different altitudes in the Colombian Andes

The stability of soil aggregates depends on the organic matter, and the soil use and management can affect the soil organicmatter (SOM) content. Therefore, it is necessary to know therelationship between aggregate stability and the content of SOMin different types of soil use at two different altitudes of theColombian Andes. This study examined the conditions of soilaggregate stability expressed as a distribution of the size classes of stable aggregates (SA) and of the mean weighted diameter of the stable aggregates (MWD). To correlate these characteristics with the soil organic carbon (OC), we measured the particulate organic matter pool (POC), the OC associated with the mineral organic matter pool (HOC), the total organic carbon content (TOC), and the humification rate (HR). Soils were sampled at two altitudes: 1) Humic Dystrudepts in a cold tropical climate (CC) with three plots: tropical mountain rainforest, pastures, and crops; 2) Fluvaquentic Dystrudepts in a warm tropical climate (WC) with three plots: tropical rainforest, an association of oil palm and pastures, and irrigated rice. Soils were sampled at three depths: 0-5, 5-10 and 10-20 cm. The physical properties, mineral particle size distribution, and bulk density were measured. The content of SA with size>2.36 mm was higher in the CC soil (51.48%) than in the WC soil (9.23%). The SA with size 1.18-2.36 mm was also higher in the CC soil (7.78%) than in the WC soil (0.62%). The SA with size 0.60-1.18 mm resulted indifferent. The SA with size between 0.30 and 0.60 mm were higher in the WC soil (13.95%) than in the CC soil (4.67%). The SA<0.30 mm was higher in the WC soil (72.56%) than in the CC soil (32.15%). It was observed that MWD and the SA>2.36 mm increased linearly with a higher POC, but decreased linearly with a higher HR. For the SA<0.30 mm, a linear decrease was observed at a higher POC, while it increased at a higher HR.

The global soil community and its influence on biogeochemistry

Soil organisms represent the most biologically diverse community on land and govern the turnover of the largest organic matter pool in the terrestrial biosphere. The highly complex nature of these communities at local scales has traditionally obscured efforts to identify unifying patterns in global soil biodiversity and biogeochemistry. As a result, environmental covariates have generally been used as a proxy to represent the variation in soil community activity in global biogeochemical models. Yet over the past decade, broad-scale studies have begun to see past this local heterogeneity to identify unifying patterns in the biomass, diversity, and composition of certain soil groups across the globe. These unifying patterns provide new insights into the fundamental distribution and dynamics of organic matter on land.

The Organic Matter Pool, Composition and Transformation in Soils of Middle Siberia

The structure and agrogenic transformation of organic substance in chernozems of Middle Siberia are considered (within Krasnoyarsk Krai, Khakassia and Tuva). The comparative-geographic, comparative-analytical and stationary observation methods are used in this work. These investigations are based on ideas of academician I.V. Tyurin, who had a Krasnoyarsk period in his creative work. All of the forms of humic compounds of chernozem type are presented in the studied soils. The mineralized (transformed) pool of organic matter in chernozems (19-28 t C/ha) is characterized by set of the plant residues, microbial biomass and a mobile humus. The entrance of plant residues into the soil of a graminae-fallow-hoed crop rotation makes 3.32 t C/ha per year, graminae-grass - 3.89 C/ha per year. The contribution of living roots reaches 40-70% of year stocks of the plant residues. The entrance of additional portions of "fresh" plant material with straw and green manure increases the mineralized pool of the organic matter and its decomposition intensity. The amount of microbial biomass in an arable layer of chernozems fluctuates from 1.5 to 3.0 t C/ha. The decomposition of plant residues occurs at k = 0.37-0.44. The share of a mobile humus (water- and alkaline-soluble compounds) as a part of the mineralized chernozems OM reaches 69-77%. The seasonal variability of mobile humus concentration is determined by the unequal rate of plants death, the entrance into the soil and decomposition of plant residues, different intensity of their transformation in neoformed humic substances. Losses of humus mobile compounds in soils of Krasnoyarsk Krai (0.23 t C/ha per year) contain about 7% of his expenses on the forming of net primary production and are compensated here by a neoformed humus at 91%, in soils of Khakassia - at 34%, Tuva - only at 16%.