Functional traits of particle-associated microbial assemblages in the low-latitude Pacific Ocean

2020 ◽  
Author(s):  
Hideto Takami ◽  
Yuya Tada ◽  
Takashi Okubo ◽  
Wataru Arai ◽  
Yoshitoshi Ogura ◽  
...  
Keyword(s):  
Organic Matter ◽  
Functional Traits ◽  
Ribosomal Proteins ◽  
Inorganic Nitrogen ◽  
Regulatory System ◽  
Bacterial Transport ◽  
Global Ocean ◽  
Transport Systems ◽  
Nutrient Regeneration ◽  
Dicarboxylate Transport

Abstract Background Organic particles are hotspots for microbial activity and serve as sites of organic matter mineralisation in the water column of marine systems. In nutrient-limited surface water, degradation of organic matter and nutrient regeneration by marine microbes is crucial. Although free-living (FL) bacteria vastly outnumber those on particles, particle-associated (PA) bacteria can reach locally higher concentrations. Accordingly, to achieve a better understanding of marine microbial ecosystems, it is important to elucidate the differences in not only microbial community structures, but also functional traits, between PA and FL environmental sample fractions. In a previous study, we demonstrated that the Genomaple (formerly MAPLE) system could successfully differentiate the functional potentials and diversity of contributors to each function in four metagenomic datasets generated by the Global Ocean Sampling expedition. Hence, we also used this system to highlight functional traits in PA microbial assemblages. Results The PA and FL fractions could be distinguished from one another by their taxonomic compositions, inferred from ribosomal proteins and relative abundance of module functions. Module functions that were more abundant among PA assemblages than FL assemblages were shared between both subtropical gyres, and their taxonomic compositions were similar. Bacterial transport systems associated with adhesive molecules used for forming microbial assemblages through particulate organic matter were more abundant in the PA fractions. Bacterial regulatory system elements for C 4 -dicarboxylate transport and B-vitamin biosynthesis were also abundant among PA assemblages, suggesting mutual relationships between bacteria and algae involved in exchange of nutrient sources. On the other hand, module functions related to amino acid biosynthesis and bacterial transport systems for inorganic nitrogen, phosphorus, and urea were significantly more abundant in the PA assemblages of more oligotrophic North and South Pacific subtropical gyres than eastern equatorial Pacific regions. Conclusions Comprehensive functional metagenomic analyses based on functional abundance revealed some notable functional traits in PA assemblages related to cell adhesion and nutrient acquisition, enabling the microbes to survive in subtropical regions that are more oligotrophic than the equatorial regions.

scholarly journals The Zinc-Responsive Regulator Zur Controls a Zinc Uptake System and Some Ribosomal Proteins in Streptomyces coelicolor A3(2)

2007 ◽  
Vol 189 (11) ◽  
pp. 4070-4077 ◽  
Author(s):  
Jung-Ho Shin ◽  
So-Young Oh ◽  
Soon-Jong Kim ◽  
Jung-Hye Roe
Keyword(s):  
Ribosomal Proteins ◽  
Streptomyces Coelicolor ◽  
Regulatory System ◽  
Repeat Sequence ◽  
Zinc Uptake ◽  
Zinc Homeostasis ◽  
Transport Systems ◽  
Binding Motif ◽  
Uptake System ◽  
Zinc Depletion

ABSTRACT In various bacteria, Zur, a zinc-specific regulator of the Fur family, regulates genes for zinc transport systems to maintain zinc homeostasis. It has also been suggested that Zur controls zinc mobilization by regulating some ribosomal proteins. The antibiotic-producing soil bacterium Streptomyces coelicolor contains four genes for Fur family regulators, and one (named zur) is located downstream of the znuACB operon encoding a putative zinc uptake transporter. We found that zinc specifically repressed the level of znuA transcripts and that this level was derepressed in a Δzur mutant. Purified Zur existing as homodimers bound to the znuA promoter region in the presence of zinc, confirming the role of Zur as a zinc-responsive repressor. We analyzed transcripts for paralogous forms of ribosomal proteins L31 (RpmE1 and RpmE2) and L33 (RpmG2 and RpmG3) for their dependence on Zur and found that RpmE2 and RpmG2 with no zinc-binding motif of conserved cysteines (C's) were negatively regulated by Zur. C-negative RpmG3 and C-positive RpmE1 were not regulated by Zur. Instead, they were regulated by the sigma factor σR as predicted from their promoter sequences. The rpmE1 and rpmG3 genes were partially induced by EDTA in a manner dependent on σR, suggesting that zinc depletion may stimulate the σR regulatory system. This finding reflects a link between thiol-oxidizing stress and zinc depletion. We determined the Zur-binding sites within znuA and rpmG2 promoter regions by footprinting analyses and identified a consensus inverted repeat sequence (TGaaAatgatTttCA, where uppercase letters represent the nucleotides common to all sites analyzed). This sequence closely matches that for mycobacterial Zur and allows the prediction of more genes in the Zur regulon.

scholarly journals Microarray Analysis of a Two-Component Regulatory System Involved in Acid Resistance and Proteolytic Activity in Lactobacillus acidophilus

2005 ◽  
Vol 71 (10) ◽  
pp. 5794-5804 ◽  
Author(s):  
M. Andrea Azcarate-Peril ◽  
Olivia McAuliffe ◽  
Eric Altermann ◽  
Sonja Lick ◽  
W. Michael Russell ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Proteolytic Activity ◽  
Lactobacillus Acidophilus ◽  
Regulatory System ◽  
Probiotic Bacterium ◽  
Transport Systems ◽  
Logarithmic Phase ◽  
Histidine Protein Kinase ◽  
Regulatory Systems ◽  
Two Component

ABSTRACT Two-component regulatory systems are one primary mechanism for environmental sensing and signal transduction. Annotation of the complete genome sequence of the probiotic bacterium Lactobacillus acidophilus NCFM revealed nine two-component regulatory systems. In this study, the histidine protein kinase of a two-component regulatory system (LBA1524HPK-LBA1525RR), similar to the acid-related system lisRK from Listeria monocytogenes (P. D. Cotter et al., J. Bacteriol. 181:6840-6843, 1999), was insertionally inactivated. A whole-genome microarray containing 97.4% of the annotated genes of L. acidophilus was used to compare genome-wide patterns of transcription at various pHs between the control and the histidine protein kinase mutant. The expression pattern of approximately 80 genes was affected by the LBA1524HPK mutation. Putative LBA1525RR target loci included two oligopeptide-transport systems present in the L. acidophilus genome, other components of the proteolytic system, and a LuxS homolog, suspected of participating in synthesis of the AI-2 signaling compound. The mutant exhibited lower tolerance to acid and ethanol in logarithmic-phase cells and poor acidification rates in milk. Supplementation of milk with Casamino Acids essentially restored the acid-producing ability of the mutant, providing additional evidence for a role of this two component system in regulating proteolytic activity in L. acidophilus.

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 ЗАКОНОМІРНОСТІ ФОРМУВАННЯ ФІТОПЛАНКТОНУ ЗА РІЗНИХ КОНЦЕНТРАЦІЙ БІОГЕННИХ ЕЛЕМЕНТІВ ТА ОРГАНІЧНОЇ РЕЧОВИНИ

2019 ◽  
Vol 75 (1) ◽  
pp. 43-51
Author(s):  
O. V. Kravtsova ◽  
V. I. Scherbak ◽  
M. I. Linchuk
Keyword(s):  
Organic Matter ◽  
Green Algae ◽  
Seasonal Dynamics ◽  
Inorganic Nitrogen ◽  
Biogenic Elements ◽  
Hydrochemical Regime ◽  
Dissolved Phosphorus ◽  
Growing Seasons ◽  
Total Inorganic Nitrogen ◽  
Plankton Communities

The seasonal dynamics of the concentration of nutrients in the form of inorganic nitrogen (NH4+, NO2, NO3-, ΣN), dissolved phosphorus, organic matter and the connection with the development of phytoplankton in waters with high content of total inorganic nitrogen (from 23.31 to 102.65 mg N/dm3) and its compounds (ammonia - from 8.42 to 76.60, nitrate - from 4.94 to 15.93, nitrite - from 0.077 to 4.35 mg N/dm3) and organic matter (from 8.00 to 21.92 mg O/dm3 by permanganate oxidation values and from 58.46 to 265.2 mg O/dm3 by dichromate oxidation values) were analyzed in paper. The peculiarity of the hydrochemical regime of the reservoirs was phenomenally high relations ΣN:P (133,54-12152,86) during the growing seasons. Found that response algal plankton communities such features hydrochemical regime is a simplification of the structure due to the predominance of representatives of departments Euglenophyta, Chlorophyta and Bacillariophyta, while Chrysophyta, Dinophyta, Charophyta and presented Cryptophyta 1-3 species. The response of phytoplankton to the high content of compounds of inorganic nitrogen is the increase in the number and biomass of green algae, and organic matter - eugenic algae.THE REGULARITIES OF PHYTOPLANKTON FORMATION AT VARIOS BIOGENIC ELEMENTS AND ORGANIC MATTER CONCENTRATIONS 

scholarly journals Photomineralization and photomethanification of dissolved organic matter in Saguenay River surface water

2015 ◽  
Vol 12 (22) ◽  
pp. 6823-6836 ◽  
Author(s):  
Y. Zhang ◽  
H. Xie
Keyword(s):  
Organic Matter ◽  
Surface Water ◽  
Dissolved Organic Matter ◽  
Dimethyl Sulfide ◽  
Ultraviolet B ◽  
Global Ocean ◽  
Quantum Yields ◽  
Methyl Radical ◽  
Ch4 Production ◽  
Saguenay River

Abstract. Rates and apparent quantum yields of photomineralization (AQYDOC) and photomethanification (AQYCH4) of chromophoric dissolved organic matter (CDOM) in Saguenay River surface water were determined at three widely differing dissolved oxygen concentrations ([O2]) (suboxic, air saturation, and oxygenated) using simulated-solar radiation. Photomineralization increased linearly with CDOM absorbance photobleaching for all three O2 treatments. Whereas the rate of photochemical dissolved organic carbon (DOC) loss increased with increasing [O2], the ratio of fractional DOC loss to fractional absorbance loss showed an inverse trend. CDOM photodegradation led to a higher degree of mineralization under suboxic conditions than under oxic conditions. AQYDOC determined under oxygenated, suboxic, and air-saturated conditions increased, decreased, and remained largely constant with photobleaching, respectively; AQYDOC obtained under air saturation with short-term irradiations could thus be applied to longer exposures. AQYDOC decreased successively from ultraviolet B (UVB) to ultraviolet A (UVA) to visible (VIS), which, alongside the solar irradiance spectrum, points to VIS and UVA being the primary drivers for photomineralization in the water column. The photomineralization rate in the Saguenay River was estimated to be 2.31 × 108 mol C yr−1, accounting for only 1 % of the annual DOC input into this system. Photoproduction of CH4 occurred under both suboxic and oxic conditions and increased with decreasing [O2], with the rate under suboxic conditions ~ 7–8 times that under oxic conditions. Photoproduction of CH4 under oxic conditions increased linearly with photomineralization and photobleaching. Under air saturation, 0.00057 % of the photochemical DOC loss was diverted to CH4, giving a photochemical CH4 production rate of 4.36 × 10−6 mol m−2 yr−1 in the Saguenay River and, by extrapolation, of (1.9–8.1) × 108 mol yr−1 in the global ocean. AQYCH4 changed little with photobleaching under air saturation but increased exponentially under suboxic conditions. Spectrally, AQYCH4 decreased sequentially from UVB to UVA to VIS, with UVB being more efficient under suboxic conditions than under oxic conditions. On a depth-integrated basis, VIS prevailed over UVB in controlling CH4 photoproduction under air saturation while the opposite held true under O2-deficiency. An addition of micromolar levels of dissolved dimethyl sulfide (DMS) substantially increased CH4 photoproduction, particularly under O2-deficiency; DMS at nanomolar ambient concentrations in surface oceans is, however, unlikely a significant CH4 precursor. Results from this study suggest that CDOM-based CH4 photoproduction only marginally contributes to the CH4 supersaturation in modern surface oceans and to both the modern and Archean atmospheric CH4 budgets, but that the photochemical term can be comparable to microbial CH4 oxidation in modern oxic oceans. Our results also suggest that anoxic microniches in particulate organic matter and phytoplankton cells containing elevated concentrations of precursors of the methyl radical such as DMS may provide potential hotspots for CH4 photoproduction.

scholarly journals Photobleaching as a factor controlling spectral characteristics of chromophoric dissolved organic matter in open ocean

2013 ◽  
Vol 10 (11) ◽  
pp. 7207-7217 ◽  
Author(s):  
Y. Yamashita ◽  
Y. Nosaka ◽  
K. Suzuki ◽  
H. Ogawa ◽  
K. Takahashi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Surface Waters ◽  
Spectral Characteristics ◽  
Open Ocean ◽  
Global Ocean ◽  
Chromophoric Dissolved Organic Matter ◽  
Spectral Slope ◽  
Subtropical Region ◽  
Subarctic Region

Abstract. Chromophoric dissolved organic matter (CDOM) ubiquitously occurs in marine environments and plays a significant role in the marine biogeochemical cycles. Basin scale distributions of CDOM have recently been surveyed in the global ocean and indicate that quantity and quality of oceanic CDOM are mainly controlled by in situ production and photobleaching. However, factors controlling the spectral parameters of CDOM in the UV region, i.e., spectral slope of CDOM determined at 275–295 nm (S275–295) and the ratio of two spectral slope parameters (SR); the ratio of S275–295 to S350–400, have not been well documented. To evaluate the factor controlling the spectral characteristics of CDOM in the UV region in the open ocean, we determined the quantitative and qualitative characteristics of CDOM in the subarctic and subtropical surface waters (5–300 m) of the western North Pacific. Absorption coefficients at 320 nm in the subarctic region were higher than those in the subtropical region throughout surface waters, suggesting that magnitudes of photobleaching were different between the two regions. The values of S275–295 and SR were also higher in the subtropical region than the subarctic region. The dark microbial incubation showed biodegradation of DOM little affected S275–295, but slightly decreased SR. On the other hand, increases in S275–295 and relative stableness of SR were observed during photo-irradiation incubations respectively. These experimental results indicated that photobleaching of CDOM mainly induced qualitative differences in CDOM at UV region between the subarctic and subtropical surface waters. The results of this study imply that S275–295 can be used as a tracer of photochemical history of CDOM in the open ocean.

EFFECTS OF NITROGEN SOURCES AND ORGANIC MATTER ON NITROGEN FIXATION AND YIELD OF SOYBEANS

1972 ◽  
Vol 52 (6) ◽  
pp. 991-996 ◽  
Author(s):  
H. S. JOHNSON ◽  
D. J. HUME
Keyword(s):  
Organic Matter ◽  
Nitrogen Fixation ◽  
Seed Yield ◽  
Inorganic Nitrogen ◽  
Nitrogen Sources ◽  
Cattle Manure ◽  
Control Treatment ◽  
Available N ◽  
Corn Cobs ◽  
Ground Corn

The effects of two sources of nitrogen and ground corn cobs, applied either alone or in combination, on nitrogen fixation and seed yield of Glycine max (L.) Merr. cult Altona were investigated in an area where control plants fixed only 7.5 kg N2/ha. Treatments were: N, 280 kg N/ha as NH4NO3; organic matter (O.M.), 14 T (dry wt)/ha of ground corn cobs as an organic matter source; N + O.M.; M1; 88 T/ha of liquid cattle manure; M1 + O.M.; M2, 176 T/ha of liquid cattle manure; M2 + O.M.; and C, control. Treatment effects on nitrogen fixation, measured as acetylene reduction rates, and seed yield were related to the levels of available N supplied to the plants. Nitrogen fixation was progressively increased by treatments M1, M2 + O.M., M1 + O.M., and O.M., with the latter two fixing seven times as much nitrogen as the control. Final seed yield, however, was increased by treatments supplying the highest levels of inorganic nitrogen to plants, with N and N + O.M. producing higher yields than the control plots.

scholarly journals Response of <i>Nodularia spumigena</i> to <i>p</i>CO<sub>2</sub> – Part 1: Growth, production and nitrogen cycling

2012 ◽  
Vol 9 (8) ◽  
pp. 2973-2988 ◽  
Author(s):  
N. Wannicke ◽  
S. Endres ◽  
A. Engel ◽  
H.-P. Grossart ◽  
M. Nausch ◽  
...  
Keyword(s):  
Organic Matter ◽  
Baltic Sea ◽  
N2 Fixation ◽  
Inorganic Nitrogen ◽  
High Pco2 ◽  
The Baltic Sea ◽  
Nodularia Spumigena ◽  
Co2 Concentrations ◽  
Elemental Stoichiometry ◽  
The Baltic

Abstract. Heterocystous cyanobacteria of the genus Nodularia form extensive blooms in the Baltic Sea and contribute substantially to the total annual primary production. Moreover, they dispense a large fraction of new nitrogen to the ecosystem when inorganic nitrogen concentration in summer is low. Thus, it is of ecological importance to know how Nodularia will react to future environmental changes, in particular to increasing carbon dioxide (CO2) concentrations and what consequences there might arise for cycling of organic matter in the Baltic Sea. Here, we determined carbon (C) and dinitrogen (N2) fixation rates, growth, elemental stoichiometry of particulate organic matter and nitrogen turnover in batch cultures of the heterocystous cyanobacterium Nodularia spumigena under low (median 315 μatm), mid (median 353 μatm), and high (median 548 μatm) CO2 concentrations. Our results demonstrate an overall stimulating effect of rising pCO2 on C and N2 fixation, as well as on cell growth. An increase in pCO2 during incubation days 0 to 9 resulted in an elevation in growth rate by 84 ± 38% (low vs. high pCO2) and 40 ± 25% (mid vs. high pCO2), as well as in N2 fixation by 93 ± 35% and 38 ± 1%, respectively. C uptake rates showed high standard deviations within treatments and in between sampling days. Nevertheless, C fixation in the high pCO2 treatment was elevated compared to the other two treatments by 97% (high vs. low) and 44% (high vs. mid) at day 0 and day 3, but this effect diminished afterwards. Additionally, elevation in carbon to nitrogen and nitrogen to phosphorus ratios of the particulate biomass formed (POC : POP and PON : POP) was observed at high pCO2. Our findings suggest that rising pCO2 stimulates the growth of heterocystous diazotrophic cyanobacteria, in a similar way as reported for the non-heterocystous diazotroph Trichodesmium. Implications for biogeochemical cycling and food web dynamics, as well as ecological and socio-economical aspects in the Baltic Sea are discussed.

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