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

2021 ◽  
Vol 8 ◽  
Author(s):  
Erin L. McParland ◽  
Harriet Alexander ◽  
Winifred M. Johnson
Keyword(s):  
Organic Matter ◽  
Organic Osmolytes ◽  
Marine Microbes ◽  
Metabolic Potential ◽  
Marine Food Webs ◽  
Homologous Protein ◽  
Carbon Demand ◽  
Production And Consumption ◽  
Organic Matter Pool ◽  
Microbial Groups

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.

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

2019 ◽  
Vol 37 (3) ◽  
pp. 263-273
Author(s):  
Efraín Francisco Visconti-Moreno ◽  
Ibonne Geaneth Valenzuela-Balcázar
Keyword(s):  
Organic Matter ◽  
Organic Carbon ◽  
Soil Organic Carbon ◽  
Aggregate Stability ◽  
Tropical Climate ◽  
Mineral Particle ◽  
Organic Carbon Content ◽  
Rice Soils ◽  
Organic Matter Pool ◽  
Different Altitudes

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.

scholarly journals Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon

2018 ◽  
Vol 85 (5) ◽  
Author(s):  
Carl-Eric Wegner ◽  
Michael Gaspar ◽  
Patricia Geesink ◽  
Martina Herrmann ◽  
Manja Marz ◽  
...  
Keyword(s):  
Land Use ◽  
Organic Matter ◽  
Groundwater Flow ◽  
Inorganic Nitrogen ◽  
Sulfur Metabolism ◽  
Ammonium Oxidation ◽  
Metabolic Potential ◽  
Differentiation Potential ◽  
Near Surface ◽  
Monitoring Wells

ABSTRACTNear-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes,Proteobacteria,Planctomycetes, andThaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCEGroundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.

scholarly journals Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

2018 ◽  
Author(s):  
Benjamin J Tully
Keyword(s):  
Organic Matter ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Diversity ◽  
Metabolic Potential ◽  
Surface Ocean ◽  
Ecological Patterns ◽  
Reference Genomes ◽  
Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

Rate of recycling of sulfur from urine, feces and litter applied to the soil surface

Soil Research ◽  
1994 ◽  
Vol 32 (3) ◽  
pp. 543 ◽  
Author(s):  
GJ Blair ◽  
AR Till ◽  
C Boswell
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Soil Surface ◽  
Plant Litter ◽  
Test Plant ◽  
Soil P ◽  
S Uptake ◽  
Organic Matter Pool ◽  
Preferential Uptake ◽  
Soil Organic Matter Pool

The recycling of S from plant litter, dung and urine is an important process for supplying S for pastures. A pot experiment was conducted where 35S-labelled litter (25% white clover/38% ryegrass/21% weed) and S-35-labelled urine and faeces collected from sheep fed the same herbage as was used as litter was surface applied to pots and the fate of the applied S was followed for 100 days with ryegrass as the test plant. In camp soil, 45% of the S applied in urine was taken up by ryegrass plants within 12 days of application. In non-camp soil, the uptake of urine-S was about 20% over the same period. Cumulative uptake of 35S from urine in camp soil was subsequently restricted, with a maximum of 60% eventually measured in plants after 100 days. Mean rates of release of S (0-37 days) from litter and faeces was respectively 16.2 and 4.5 mg g-1 day-1. The calculated half-times from S in the two materials were respectively 43 and 154 days under controlled environmental conditions with adequate moisture. Litter S followed organic matter (OM) decomposition, but faecal S release was initially more rapid than faecal OM decomposition. There was little S release from faeces after day 25. Rather, S was immobilized in faeces during the 25-100 day period. The decomposition of litter and faeces was divided into an initial rapid process during which soluble S and more labile S was released, followed by a slower process involving the release of S from tissues more resistant to mineralization. The uptake of 35S from labelled materials was initially more rapid than would be expected for total S released from the added litter and faeces and the 35Suptake effect was short-lived relative to the continued effect of added material on total S uptake. The preferential uptake of 35S from the surface-applied material appears to be due to limited root development at the early stages of the experiment. Movement of 35S into the soil organic matter pool was very rapid; 58.4% of urine S was in the soil organic matter fraction in the non-camp soil by day 6. The amount of applied S in the organic matter equilibrated at about day 75. The accumulation of applied S from the materials added was greater than that recorded in previously reported studies for inorganic sulfate (e.g. about 50%). Soil P and S status had little effect on rates of release of S. from the applied materials, however, the effect of the camp and non-camp soil on total S recycling was markedly different as a result of the different amounts of plant growth and thus S uptake in the two soils. The decomposition of litter indicated peak rates of S release at two specific times over the 100 days and indicated successional changes in micro-organism activity. With faeces, the experiment was not continued for sufficiently long to show micro-organism effects.

Features of algae tests of samples containing dissolved organic matter

2020 ◽  
pp. 40-45
Author(s):  
Elena V. Fedoseeva ◽  
Iya Yu. Grigorieva ◽  
Olga V. Nikolaeva ◽  
Vera A. Terekhova
Keyword(s):  
Organic Matter ◽  
Chlorophyll Fluorescence ◽  
Dissolved Organic Matter ◽  
Marine Algae ◽  
Cultivation Conditions ◽  
High Reproducibility ◽  
Test Culture ◽  
Production And Consumption ◽  
Number Of Cells ◽  
Consumption Waste

Algae tests are widely used due to the availability of cultivation conditions and high reproducibility. Freshwater and marine algae are used to estimate the toxicity of drinking, natural and wastewater, water extracts from soils, sewage sludge and production and consumption waste. The presence of dissolved organic matter in the samples, stimulating the growth of algae and the intensity of chlorophyll fluorescence, can significantly affect the result of algae tests, and therefore on the decision on the presence or absence of a toxic effect. When choosing algae as a test culture to determine toxic effects, it is necessary to take into account the possibility of hyperstimulating the number of cells with dissolved organic matter.

scholarly journals The global soil community and its influence on biogeochemistry

Science ◽  
2019 ◽  
Vol 365 (6455) ◽  
pp. eaav0550 ◽  
Author(s):  
T. W. Crowther ◽  
J. van den Hoogen ◽  
J. Wan ◽  
M. A. Mayes ◽  
A. D. Keiser ◽  
...  
Keyword(s):  
Organic Matter ◽  
Complex Nature ◽  
Soil Biodiversity ◽  
Soil Community ◽  
The Past ◽  
Biogeochemical Models ◽  
Global Soil ◽  
Organic Matter Pool ◽  
Diverse Community ◽  
Soil Groups

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.

scholarly journals Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

2020 ◽  
Vol 8 (9) ◽  
pp. 1412
Author(s):  
Minji Kim ◽  
In-Tae Cha ◽  
Ki-Eun Lee ◽  
Eun-Young Lee ◽  
Soo-Je Park
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Extracellular Enzymes ◽  
Marine Invertebrates ◽  
Carbon Sources ◽  
Marine Environments ◽  
Metabolic Potential ◽  
Carbohydrate Utilization ◽  
Genes Encoding ◽  
Metagenomic Study

Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

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