Interesting anaerobes in the environment

Prokaryotes (Bacteria and Archaea) have a wide range of capacities to survive by generating energy in environments and situations lacking oxygen, which abound on Earth. Anaerobic metabolic strategies include anaerobic respiration (numerous types – e.g. nitrate reduction – Paracoccus denitrificans; sulfur respiration – Desulfuromonadales; methanogenesis – Methanosarsina spp.; iron reduction – Geobacter spp.; dehalorespiration – Dehalococcoides ethenogenes) and fermentation (sugars converted to simpler organic compounds like acids, gases and alcohols – e.g. Lactobacillus spp.). Relatively novel environmental anaerobic strategies include anaerobic ammonium oxidation (Anammox – e.g. Brocadia spp.) and anaerobic methane oxidation (AMO)1, which is a syntrophic association between anaerobic methanotrophic archaea (ANME) and sulfate-, iron-, manganese- or nitrate-reducing bacteria2. The classic anaerobic synthrophic example is interspecies hydrogen/formate transfer between a hydrogen/formate producing fatty acid oxidising bacterium (the syntroph) and a hydrogen/formate consumer (methanogen or sulfate-reducer)3. Microbes vary in their oxygen tolerance and are described as obligate anaerobes if they are killed by atmospheric levels of oxygen due to the lack of catalase and superoxide dismutase that provide oxygen radical protection.

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Insights Gained from the Dehalococcoides ethenogenes" Strain 195's Transcriptome Responding to a Wide Range of Respiration Rates and Substrate Types"

10.21236/ada559475 ◽

2012 ◽

Author(s):

Cresten Manfeldt ◽

Annette Rowe ◽

Gretchen Heavner ◽

Stephen Zinder ◽

Ruth Richardson

Keyword(s):

Respiration Rates ◽

Dehalococcoides Ethenogenes ◽

Wide Range ◽

Substrate Types

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From Residues to Added-Value Bacterial Biopolymers as Nanomaterials for Biomedical Applications

Nanomaterials ◽

10.3390/nano11061492 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1492

Author(s):

Francisco G. Blanco ◽

Natalia Hernández ◽

Virginia Rivero-Buceta ◽

Beatriz Maestro ◽

Jesús M. Sanz ◽

...

Keyword(s):

Biomedical Applications ◽

Carbon Sources ◽

Structural Diversity ◽

Added Value ◽

Nanoscale Systems ◽

Chemical Structures ◽

Wide Range ◽

Peptide Functionalization ◽

Metabolic Strategies ◽

Drug Nanocarriers

Bacterial biopolymers are naturally occurring materials comprising a wide range of molecules with diverse chemical structures that can be produced from renewable sources following the principles of the circular economy. Over the last decades, they have gained substantial interest in the biomedical field as drug nanocarriers, implantable material coatings, and tissue-regeneration scaffolds or membranes due to their inherent biocompatibility, biodegradability into nonhazardous disintegration products, and their mechanical properties, which are similar to those of human tissues. The present review focuses upon three technologically advanced bacterial biopolymers, namely, bacterial cellulose (BC), polyhydroxyalkanoates (PHA), and γ-polyglutamic acid (PGA), as models of different carbon-backbone structures (polysaccharides, polyesters, and polyamides) produced by bacteria that are suitable for biomedical applications in nanoscale systems. This selection models evidence of the wide versatility of microorganisms to generate biopolymers by diverse metabolic strategies. We highlight the suitability for applied sustainable bioprocesses for the production of BC, PHA, and PGA based on renewable carbon sources and the singularity of each process driven by bacterial machinery. The inherent properties of each polymer can be fine-tuned by means of chemical and biotechnological approaches, such as metabolic engineering and peptide functionalization, to further expand their structural diversity and their applicability as nanomaterials in biomedicine.

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Iron and Carbon Isotope Constraints on the Formation Pathway of Iron-Rich Carbonates within the Dagushan Iron Formation, North China Craton

Minerals ◽

10.3390/min11010094 ◽

2021 ◽

Vol 11 (1) ◽

pp. 94

Author(s):

Xiaoxue Tong ◽

Kaarel Mänd ◽

Yuhao Li ◽

Lianchang Zhang ◽

Zidong Peng ◽

...

Keyword(s):

Iron Reduction ◽

Isotope Composition ◽

Iron Formation ◽

Banded Iron Formations ◽

Organic C ◽

Formation Pathway ◽

Wide Range ◽

Dissimilatory Iron Reduction ◽

O Isotope ◽

Iron Formations

Banded iron formations (BIFs) are enigmatic chemical sedimentary rocks that chronicle the geochemical and microbial cycling of iron and carbon in the Precambrian. However, the formation pathways of Fe carbonate, namely siderite, remain disputed. Here, we provide photomicrographs, Fe, C and O isotope of siderite, and organic C isotope of the whole rock from the ~2.52 Ga Dagushan BIF in the Anshan area, China, to discuss the origin of siderite. There are small magnetite grains that occur as inclusions within siderite, suggesting a diagenetic origin of the siderite. Moreover, the siderites have a wide range of iron isotope compositions (δ56FeSd) from −0.180‰ to +0.463‰, and a relatively negative C isotope composition (δ13CSd = −6.20‰ to −1.57‰). These results are compatible with the reduction of an Fe(III)-oxyhydroxide precursor to dissolved Fe(II) through microbial dissimilatory iron reduction (DIR) during early diagenesis. Partial reduction of the precursor and possible mixing with seawater Fe(II) could explain the presence of siderite with negative δ56Fe, while sustained reaction of residual Fe(III)-oxyhydroxide could have produced siderite with positive δ56Fe values. Bicarbonate derived from both DIR and seawater may have provided a C source for siderite formation. Our results suggest that microbial respiration played an important role in the formation of siderite in the late Archean Dagushan BIF.

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Remedial Treatment of Corroded Iron Objects by EnvironmentalAeromonasIsolates

Applied and Environmental Microbiology ◽

10.1128/aem.02042-18 ◽

2018 ◽

Vol 85 (3) ◽

Cited By ~ 1

Author(s):

Wafa M. Kooli ◽

Thomas Junier ◽

Migun Shakya ◽

Mathilde Monachon ◽

Karen W. Davenport ◽

...

Keyword(s):

Iron Reduction ◽

Building Materials ◽

Solid Phase ◽

Corrosion Products ◽

Metal Corrosion ◽

Economic Losses ◽

Cytotoxic Activities ◽

Iron Corrosion ◽

Pathogenic Potential ◽

Wide Range

ABSTRACTUsing bacteria to transform reactive corrosion products into stable compounds represents an alternative to traditional methods employed in iron conservation. Two environmentalAeromonasstrains (CA23 and CU5) were used to transform ferric iron corrosion products (goethite and lepidocrocite) into stable ferrous iron-bearing minerals (vivianite and siderite). A genomic and transcriptomic approach was used to analyze the metabolic traits of these strains and to evaluate their pathogenic potential. Although genes involved in solid-phase iron reduction were identified, key genes present in other environmental iron-reducing species are missing from the genome of CU5. Several pathogenicity factors were identified in the genomes of both strains, but none of these was expressed under iron reduction conditions. Additionalin vivotests showed hemolytic and cytotoxic activities for strain CA23 but not for strain CU5. Both strains were easily inactivated using ethanol and heat. Nonetheless, given a lesser potential for a pathogenic lifestyle, CU5 is the most promising candidate for the development of a bio-based iron conservation method stabilizing iron corrosion. Based on all the results, a prototype treatment was established using archaeological items. On those, the conversion of reactive corrosion products and the formation of a homogenous layer of biogenic iron minerals were achieved. This study shows how naturally occurring microorganisms and their metabolic capabilities can be used to develop bio-inspired solutions to the problem of metal corrosion.IMPORTANCEMicrobiology can greatly help in the quest for a sustainable solution to the problem of iron corrosion, which causes important economic losses in a wide range of fields, including the protection of cultural heritage and building materials. Using bacteria to transform reactive and unstable corrosion products into more-stable compounds represents a promising approach. The overall aim of this study was to develop a method for the conservation and restoration of corroded iron items, starting from the isolation of iron-reducing bacteria from natural environments. This resulted in the identification of a suitable candidate (Aeromonassp. strain CU5) that mediates the formation of desirable minerals at the surfaces of the objects. This led to the proof of concept of an application method on real objects.

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Nitrogen Loss through Anaerobic Ammonium Oxidation Coupled to Iron Reduction from Paddy Soils in a Chronosequence

Environmental Science & Technology ◽

10.1021/es503113s ◽

2014 ◽

Vol 48 (18) ◽

pp. 10641-10647 ◽

Cited By ~ 104

Author(s):

Long-Jun Ding ◽

Xin-Li An ◽

Shun Li ◽

Gan-Lin Zhang ◽

Yong-Guan Zhu

Keyword(s):

Iron Reduction ◽

Nitrogen Loss ◽

Anaerobic Ammonium Oxidation ◽

Paddy Soils ◽

Ammonium Oxidation

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Recovery of Phosphorus from Waste Water Profiting from Biological Nitrogen Treatment: Upstream, Concomitant or Downstream Precipitation Alternatives

Agronomy ◽

10.3390/agronomy10071039 ◽

2020 ◽

Vol 10 (7) ◽

pp. 1039

Author(s):

Albert Magrí ◽

Mar Carreras-Sempere ◽

Carmen Biel ◽

Jesús Colprim

Keyword(s):

Waste Water ◽

Water Treatment ◽

Waste Water Treatment ◽

N Recovery ◽

Ammonium Oxidation ◽

Chemically Induced ◽

Wide Range ◽

N Treatment ◽

Phosphate Salts ◽

Biological Nitrogen

Mined phosphate rock is the largest source of phosphorus (P) for use in agriculture and agro-industry, but it also is a finite resource irregularly distributed around the world. Alternatively, waste water is a renewable source of P, available at the local scale. In waste water treatment, biological nitrogen (N) removal is applied according to a wide range of variants targeting the abatement of the ammonium content. Ammonium oxidation to nitrate can also be considered to mitigate ammonia emission, while enabling N recovery. This review focuses on the analysis of alternatives for coupling biological N treatment and phosphate precipitation when treating waste water in view of producing P-rich materials easily usable as fertilisers. Phosphate precipitation can be applied before (upstream configuration), together with (concomitant configuration), and after (downstream configuration) N treatment; i.e., chemically induced as a conditioning pre-treatment, biologically induced inside the reactor, and chemically induced as a refining post-treatment. Characteristics of the recovered products differ significantly depending on the case studied. Currently, precipitated phosphate salts are not typified in the European fertiliser regulation, and this fact limits marketability. Nonetheless, this topic is in progress. The potential requirements to be complied by these materials to be covered by the regulation are overviewed. The insights given will help in identifying enhanced integrated approaches for waste water treatment, pointing out significant needs for subsequent agronomic valorisation of the recovered phosphate salts, according to the paradigms of the circular economy, sustainability, and environmental protection.

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Cumate-Inducible Gene Expression System for Sphingomonads and Other Alphaproteobacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02296-13 ◽

2013 ◽

Vol 79 (21) ◽

pp. 6795-6802 ◽

Cited By ~ 40

Author(s):

Andreas Kaczmarczyk ◽

Julia A. Vorholt ◽

Anne Francez-Charlot

Keyword(s):

Gene Expression ◽

Caulobacter Crescentus ◽

Paracoccus Denitrificans ◽

Expression System ◽

Model Organisms ◽

Inducible Gene Expression ◽

Gene Expression System ◽

Content Type ◽

Wide Range ◽

Inducible Gene

ABSTRACTTunable promoters represent a pivotal genetic tool for a wide range of applications. Here we present such a system for sphingomonads, a phylogenetically diverse group of bacteria that have gained much interest for their potential in bioremediation and their use in industry and for which no dedicated inducible gene expression system has been described so far. A strong, constitutive synthetic promoter was first identified through a genetic screen and subsequently combined with the repressor and the operator sites of thePseudomonas putidaF1cym/cmtsystem. The resulting promoter, termed PQ5, responds rapidly to the inducer cumate and shows a maximal induction ratio of 2 to 3 orders of magnitude in the different sphingomonads tested. Moreover, it was also functional in otherAlphaproteobacteria, such as the model organismsCaulobacter crescentus,Paracoccus denitrificans, andMethylobacterium extorquens. In the noninduced state, expression from PQ5is low enough to allow gene depletion analysis, as demonstrated with the essential genephyPofSphingomonassp. strain Fr1. A set of PQ5-based plasmids has been constructed allowing fusions to affinity tags or fluorescent proteins.

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Modeling anaerobic soil organic carbon decomposition in Arctic polygon tundra: insights into soil geochemical influences on carbon mineralization

Biogeosciences ◽

10.5194/bg-16-663-2019 ◽

2019 ◽

Vol 16 (3) ◽

pp. 663-680 ◽

Cited By ~ 7

Author(s):

Jianqiu Zheng ◽

Peter E. Thornton ◽

Scott L. Painter ◽

Baohua Gu ◽

Stan D. Wullschleger ◽

...

Keyword(s):

Temperature Sensitivity ◽

Iron Reduction ◽

Carbon Mineralization ◽

Co2 Production ◽

Model Framework ◽

Binding Model ◽

Microbial Decomposition ◽

Carbon Decomposition ◽

Ch4 Production ◽

Wide Range

Abstract. Rapid warming of Arctic ecosystems exposes soil organic matter (SOM) to accelerated microbial decomposition, potentially leading to increased emissions of carbon dioxide (CO2) and methane (CH4) that have a positive feedback on global warming. Current estimates of the magnitude and form of carbon emissions from Earth system models include significant uncertainties, partially due to the oversimplified representation of geochemical constraints on microbial decomposition. Here, we coupled modeling principles developed in different disciplines, including a thermodynamically based microbial growth model for methanogenesis and iron reduction, a pool-based model to represent upstream carbon transformations, and a humic ion-binding model for dynamic pH simulation to build a more versatile carbon decomposition model framework that can be applied to soils under varying redox conditions. This new model framework was parameterized and validated using synthesized anaerobic incubation data from permafrost-affected soils along a gradient of fine-scale thermal and hydrological variabilities across Arctic polygonal tundra. The model accurately simulated anaerobic CO2 production and its temperature sensitivity using data on labile carbon pools and fermentation rates as model constraints. CH4 production is strongly influenced by water content, pH, methanogen biomass, and presence of competing electron acceptors, resulting in high variability in its temperature sensitivity. This work provides new insights into the interactions of SOM pools, temperature increase, soil geochemical feedbacks, and resulting CO2 and CH4 production. The proposed anaerobic carbon decomposition framework presented here builds a mechanistic link between soil geochemistry and carbon mineralization, making it applicable over a wide range of soils under different environmental settings.

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Constraints on Anaerobic Respiration in the Hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum

Applied and Environmental Microbiology ◽

10.1128/aem.02033-07 ◽

2007 ◽

Vol 74 (2) ◽

pp. 396-402 ◽

Cited By ~ 22

Author(s):

Lawrence F. Feinberg ◽

R. Srikanth ◽

Richard W. Vachet ◽

James F. Holden

Keyword(s):

Iron Oxide ◽

Growth Rates ◽

Direct Contact ◽

Iron Reduction ◽

Elemental Sulfur ◽

Reductase Activity ◽

Anaerobic Respiration ◽

Hyperthermophilic Archaea ◽

Pyrobaculum Aerophilum ◽

Pyrobaculum Islandicum

ABSTRACT Pyrobaculum islandicum uses iron, thiosulfate, and elemental sulfur for anaerobic respiration, while Pyrobaculum aerophilum uses iron and nitrate; however, the constraints on these processes and their physiological mechanisms for iron and sulfur reduction are not well understood. Growth rates on sulfur compounds are highest at pH 5 to 6 and highly reduced (<−420-mV) conditions, while growth rates on nitrate and iron are highest at pH 7 to 9 and more-oxidized (>−210-mV) conditions. Growth on iron expands the known pH range of growth for both organisms. P. islandicum differs from P. aerophilum in that it requires direct contact with insoluble iron oxide for growth, it did not produce any extracellular compounds when grown on insoluble iron, and it lacked 2,6-anthrahydroquinone disulfonate oxidase activity. Furthermore, iron reduction in P. islandicum appears to be completely independent of c-type cytochromes. Like that in P. aerophilum, NADH-dependent ferric reductase activity in P. islandicum increased significantly in iron-grown cultures relative to that in non-iron-grown cultures. Proteomic analyses showed that there were significant increases in the amounts of a putative membrane-bound thiosulfate reductase in P. islandicum cultures grown on thiosulfate relative to those in cultures grown on iron and elemental sulfur. This is the first evidence of this enzyme being used in either a hyperthermophile or an archaeon. Pyrobaculum arsenaticum and Pyrobaculum calidifontis also grew on Fe(III) citrate and insoluble iron oxide, but only P. arsenaticum could grow on insoluble iron without direct contact.

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