Eco-physiology of autotrophic nitrifying biofilms

2005 ◽  
Vol 52 (7) ◽  
pp. 225-232 ◽  
Author(s):  
S. Okabe ◽  
T. Kindaichi ◽  
Y. Nakamura ◽  
T. Ito
Keyword(s):  
Organic Matter ◽  
Fluorescent In Situ Hybridization ◽  
Direct Evidence ◽  
Heterotrophic Bacteria ◽  
Microbial Interactions ◽  
Nitrifying Bacteria ◽  
Low Molecular Weight ◽  
Sulfur Bacteria ◽  
First Time

Microautoradiography combined with fluorescent in situ hybridization (MAR-FISH), a powerful tool for linking physiology with identification of individual cells, was applied to investigate microbial interactions between nitrifying bacteria and coexisting heterotrophic bacteria in an autotrophic nitrifying biofilm community fed with only ammonia as the sole energy source and bicarbonate as the sole carbon source. First, nitrifying bacteria were radiolabeled by culturing the biofilm samples with [14C]bicarbonate for 6 h, and then the transfer of radioactivity from nitrifying bacteria to heterotrophic bacteria was monitored by using MAR-FISH. MAR-FISH revealed that the heterotrophic bacterial community was composed of bacteria that were phylogenetically and metabolically diverse. We could obtain direct evidence that organic matter derived from nitrifiers was subsequently utilized by mainly filamentous bacteria belonging to the Chloroflexi (green non-sulfur bacteria) group or CFB group in the biofilm, which was clearly visualized by MAR-FISH at single cell resolution for the first time. On the other hand, the members of the α- and γ-Proteobacteria were specialized to utilize low-molecular-weight organic matter. This community represents functionally integrated units that assure maximum access to and utilization of metabolites of nitrifiers.

scholarly journals Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiang Zheng ◽  
Yu Wang ◽  
Jiayao Lu ◽  
Wenxin Lin ◽  
Feng Chen ◽  
...  
Keyword(s):  
Organic Matter ◽  
Bacterial Community ◽  
Heterotrophic Bacteria ◽  
Bacterial Community Composition ◽  
Complex Compounds ◽  
Transport Systems ◽  
Bacterial Strains ◽  
Bacterial Populations ◽  
Coculture System

ABSTRACT Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes, including Synechococcus and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the Synechococcus-heterotroph coculture system and the interactions shaping the system. IMPORTANCE The high complexity of in situ ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of in situ environments.

In situ formation of AuNPs using fatty N-acylamino hydrazide organogelators as templates

2019 ◽  
Vol 43 (1) ◽  
pp. 295-303 ◽  
Author(s):  
Renata Ongaratto ◽  
Naiane Conte ◽  
Caroline R. Montes D’Oca ◽  
Rafael C. Brinkerhoff ◽  
Caroline Pires Ruas ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Gold Nanoparticles ◽  
Low Molecular Weight ◽  
In Situ Formation ◽  
First Time

This work reports, for the first time, the synthesis of new fatty N-acylamino hydrazides and demonstrates the activity of these compounds as low-molecular-weight organic gelators and templates for preparation of gold nanoparticles (AuNPs).

scholarly journals Seasonal Population Dynamics and Interactions of Competing Bacteriophages and Their Host in the Rhizosphere

2000 ◽  
Vol 66 (10) ◽  
pp. 4193-4199 ◽  
Author(s):  
Kevin E. Ashelford ◽  
Susan J. Norris ◽  
John C. Fry ◽  
Mark J. Bailey ◽  
Martin J. Day
Keyword(s):  
Sugar Beet ◽  
Latin Square ◽  
Optimal Foraging Theory ◽  
Microbial Interactions ◽  
Phage Ecology ◽  
Competitive Disadvantage ◽  
First Time ◽  
Field Plots ◽  
Seasonal Population

ABSTRACT We describe two prolonged bacteriophage blooms within sugar beet rhizospheres ensuing from an artificial increase in numbers of an indigenous soil bacterium. Further, we provide evidence of in situ competition between these phages. This is the first in situ demonstration of such microbial interactions in soil. To achieve this, sugar beet seeds were inoculated with Serratia liquefaciensCP6RS or its lysogen, CP6RS-ly-Φ1. These were sown, along with uninoculated seeds, in 36 field plots arranged in a randomized Latin square. The plots were then sampled regularly over 194 days, and the plants were assayed for the released bacteria and any infectious phages. Both the lysogen and nonlysogen forms of CP6RS survived equally well in situ, contradicting earlier work suggesting lysogens have a competitive disadvantage in nature. A Podoviridae phage, identified as ΦCP6-4, flourished on the nonlysogen-inoculated plants in contrast to those plants inoculated with the lysogen. Conversely, the Siphoviridae phage ΦCP6-1 (used to construct the released lysogen) was isolated abundantly from the lysogen-treated plants but almost never on the nonlysogen-inoculated plants. The uninoculated plants also harbored some ΦCP6-1 phage up to day 137, yet hardly any ΦCP6-4 phages were found, and this was consistent with previous years. We show that the different temporal and spatial distributions of these two physiologically distinct phages can be explained by application of optimal foraging theory to phage ecology. This is the first time that such in situ evidence has been provided in support of this theoretical model.

scholarly journals Fractal aggregation and disaggregation of newly formed iron(iii) (hydr)oxide nanoparticles in the presence of natural organic matter and arsenic

2016 ◽  
Vol 3 (3) ◽  
pp. 647-656 ◽  
Author(s):  
Chelsea W. Neil ◽  
Jessica R. Ray ◽  
Byeongdu Lee ◽  
Young-Shin Jun
Keyword(s):  
Organic Matter ◽  
Natural Organic Matter ◽  
Oxide Nanoparticles ◽  
Aggregation And Disaggregation ◽  
First Time

This study provides for the first timein situobservations of organic matter and arsenic effects on iron(iii) (hydr)oxide precipitation.

scholarly journals Performance and bacterial diversity of bioreactors used for simultaneous removal of sulfide, solids and organic matter from UASB reactor effluents

2018 ◽  
Vol 78 (6) ◽  
pp. 1312-1323 ◽  
Author(s):  
L. S. Azevedo ◽  
I. M. P. Castro ◽  
C. D. Leal ◽  
J. C. Araújo ◽  
C. A. L. Chernicharo
Keyword(s):  
Organic Matter ◽  
Elemental Sulfur ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Heterotrophic Bacteria ◽  
Packing Material ◽  
Post Treatment ◽  
Upflow Anaerobic Sludge Blanket ◽  
Uasb Reactor ◽  
Anaerobic Sludge ◽  
Sulfur Bacteria

Abstract Two bioreactors were investigated as an alternative to post-treatment of effluent from an upflow anaerobic sludge blanket (UASB) reactor treating domestic sewage, with an aim of oxidizing sulfide into elemental sulfur, and removal of solid and organic material. The bioreactors were operated at different hydraulic retention times (HRTs) (6, 4, and 2 h) and in the presence or absence (control) of packing material (polypropylene rings). Greater sulfide removal efficiencies – 75% (control reactor) and 92% (packed reactor) – were achieved in both reactors for an HRT of 6 h. Higher organic matter (COD) and solid (TSS) removal levels were observed in the packed reactor, which produced effluent with low COD (100 mg CODL−1) and TSS concentrations (30 mg TSSL−1). Denaturing gradient gel electrophoresis results revealed that a metabolically diverse bacterial community was present in both bioreactors, with sequences related to heterotrophic bacteria, sulfur bacteria (Thiocapsa, Sulfurimonas sp., Chlorobaculum sp., Chromatiales and Sulfuricellales), phototrophic purple non-sulfur bacteria (Rhodopseudomonas, Rhodocyclus sp.) and cyanobacteria. The packed reactor presented higher extracellular sulfur formation and potential for elemental sulfur recovery was seen. Higher efficiencies related to the packed reactor were attributed to the presence of packing material and higher cell retention time. The studied bioreactors seemed to be a simple and low-cost alternative for the post-treatment of anaerobic effluent.

scholarly journals Diel dynamics of dissolved organic matter and heterotrophic prokaryotes reveal enhanced growth at the ocean’s mesopelagic fish layer during daytime

2019 ◽  
Author(s):  
Xosé Anxelu G. Morán ◽  
Francisca C. García ◽  
Anders Røstad ◽  
Luis Silva ◽  
Najwa Al-Otaibi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Heterotrophic Bacteria ◽  
Mesopelagic Fish ◽  
Diel Cycles ◽  
Organic Carbon Concentration ◽  
Mesopelagic Zone ◽  
Heterotrophic Prokaryotes ◽  
Specific Growth Rates

ABSTRACTContrary to epipelagic waters, where biogeochemical processes closely follow the light and dark periods, little is known about diel cycles in the ocean’s mesopelagic realm. Here, we monitored the dynamics of dissolved organic matter (DOM) and planktonic heterotrophic prokaryotes every 2 h for one day at 0 and 550 m (a depth occupied by vertically migrating fish during light hours) in oligotrophic waters of the central Red Sea. We additionally performed predator-free seawater incubations of samples collected from the same site both at midnight and at noon. Comparable in situ variability in microbial biomass and dissolved organic carbon concentration suggests a diel supply of fresh DOM in both layers. The presence of fish in the mesopelagic zone during daytime promoted a sustained, longer growth of larger prokaryotic cells. The specific growth rates were consistently higher in the noon experiments from both depths (surface: 0.34 vs. 0.18 d−1, mesopelagic: 0.16 vs. 0.09 d−1). Heterotrophic bacteria and archaea in the mesopelagic fish layer were also more efficient at converting DOM into new biomass. These results suggest that the ocean’s twilight zone receives a consistent diurnal supply of labile DOM from diel vertical migrating fishes, enabling an unexpectedly active community of heterotrophic prokaryotes.

scholarly journals Ooids forming in situ within microbial mats (Kiritimati atoll, central Pacific)

PalZ ◽  
2021 ◽  
Author(s):  
Pablo Suarez-Gonzalez ◽  
Joachim Reitner
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Microbial Mats ◽  
Formation Processes ◽  
Central Pacific ◽  
Environmental Processes ◽  
Definition Of ◽  
First Time

AbstractOoids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here, we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but these particles grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of the term ‘ooid’ and are in fact very similar to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which leads to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.

Significance of substrate C/N ratio on structure and activity of nitrifying biofilms determined by in situ hybridization and the use of microelectrodes

2000 ◽  
Vol 41 (4-5) ◽  
pp. 317-321 ◽  
Author(s):  
H. Satoh ◽  
S. Okabe ◽  
N. Norimatsu ◽  
Y. Watanabe
Keyword(s):  
In Situ Hybridization ◽  
Heterotrophic Bacteria ◽  
Outer Part ◽  
Experimental Result ◽  
Nitrifying Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
Spatial Distributions ◽  
Interspecies Competition ◽  
Oxidation Rates

The effect of substrate C/N ratio on the spatial distributions of ammonia-oxidizing bacteria and their activity was investigated by using microelectrodes with high spatial resolution and fluorescent in situ hybridization (FISH) technique. In this study, an interspecies competition for O2 between ammonia-oxidizing bacteria and heterotrophic bacteria was experimentally evaluated. An autotrophic nitrifying biofilm originally cultured at C/N=0 was used as a model biofilm to study changes in specific NH4+ oxidation rate profiles in the biofilm when the substrate C/N ratio was varied. As C/N ratio increased, specific NH4+ oxidation rates decreased in the outer part of the biofilm due to interspecies competition, while they were unchanged in the inner part. The increase in substrate C/N ratio (i.e., addition of acetate) immediately induced the interspecies competition for O2 between ammonia-oxidizing bacteria and heterotrophic bacteria at the outer part of the biofilm. As a result of the interspecies competition, NH4plus; oxidation was restrained, resulting in a decrease in the ammonia-oxidizing bacterial populations. This experimental result clearly explains the stratified spatial distributions of ammonia-oxidizing bacteria within the biofilms at higher substrate C/N ratios. The combined application of microelectrodes and FISH techniques provides new insights into microbial ecology and population dynamics of nitrifying bacteria within multi-species biofilms.

scholarly journals Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Miriam Philippi ◽  
Katharina Kitzinger ◽  
Jasmine S. Berg ◽  
Bernhard Tschitschko ◽  
Abiel T. Kidane ◽  
...  
Keyword(s):  
Single Cell ◽  
Direct Evidence ◽  
Early Earth ◽  
Purple Sulfur Bacteria ◽  
Continental Margins ◽  
Sulfur Bacteria ◽  
Analogue System

AbstractBiological N2 fixation was key to the expansion of life on early Earth. The N2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N2 fixation in the Proterozoic ocean.

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