Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities

Biofilms as Battlefield Armor for Bacteria against Antibiotics: Challenges and Combating Strategies

Bacterial biofilms are formed by communities, which are encased in a matrix of extracellular polymeric substances (EPS). Notably, bacteria in biofilms display a set of 'emergent properties' that vary considerably from free-living bacterial cells. Biofilms help bacteria to survive under multiple stressful conditions such as providing immunity against antibiotics. Apart from the provision of multi-layered defense for enabling poor antibiotic absorption and adaptive persistor cells, biofilms utilize their extracellular components, e.g., extracellular DNA (eDNA), chemical-like catalase, various genes and their regulators to combat antibiotics. The response of biofilms depends on the type of antibiotic that comes into contact with biofilms. For example, excessive production of eDNA exerts resistance against cell wall and DNA targeting antibiotics and the release of antagonist chemicals neutralizes cell membrane inhibitors, whereas the induction of protein and folic acid antibiotics inside cells is lowered by mutating genes and their regulators. Here, we review the current state of knowledge of biofilm-based resistance to various antibiotic classes in bacteria and genes responsible for biofilm development, and the key role of quorum sensing in developing biofilms and antibiotic resistance is also discussed. In this review, we also highlight new and modified techniques such as CRISPR/Cas, nanotechnology and bacteriophage therapy. These technologies might be useful to eliminate pathogens residing in biofilms by combating biofilm-induced antibiotic resistance and making this world free of antibiotic resistance.

Advancements in antimicrobial nanoscale materials and self-assembling systems

Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.

Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A

Abstract

Bioleaching of metal sulfides is performed by diverse microorganisms. The dissolution of metal sulfides occurs via two chemical pathways, either the thiosulfate or the polysulfide pathway. These are determined by the metal sulfides’ mineralogy and their acid solubility. The microbial cell enables metal sulfide dissolution via oxidation of iron(II) ions and inorganic sulfur compounds. Thereby, the metal sulfide attacking agents iron(III) ions and protons are generated. Cells are active either in a planktonic state or attached to the mineral surface, forming biofilms. This review, as an update of the previous one (Vera et al., 2013a), summarizes some recent discoveries relevant to bioleaching microorganisms, contributing to a better understanding of their lifestyle. These comprise phylogeny, chemical pathways, surface science, biochemistry of iron and sulfur metabolism, anaerobic metabolism, cell–cell communication, molecular biology, and biofilm lifestyle. Recent advances from genetic engineering applied to bioleaching microorganisms will allow in the future to better understand important aspects of their physiology, as well as to open new possibilities for synthetic biology applications of leaching microbial consortia.

Key points

• Leaching of metal sulfides is strongly enhanced by microorganisms

• Biofilm formation and extracellular polymer production influences bioleaching

• Cell interactions in mixed bioleaching cultures are key for process optimization

Insight into dead space effects in granular anammox process with organic stress

In this study, the dead space was demonstrated to enhance the robustness of anammox nitrogen (N)-removal under organic stress. Different from the "yellow aggregates" that inhabit in mixing space were assembled by anammox and heterotrophic micro-colonies, the "red granules" that inhabit in dead space were formed by initial anammox aggregates that growing outward with higher anammox-activity, settleability and sludge stability, which endowed the dead space the role of "anammox-stabilizer" with prominent anammox N-removal contribution (63.8%) especially under high organic stress. The extracellular polymeric substances (EPS) dynamic balance test revealed that the high and stable EPS contents in dead space were attributed to the low EPS degradation rate and low proportion of heterotrophic bacteria (HB)-produced EPS, respectively. The weak hydrodynamic forces were the key to less HB-colonization and high granular stability in dead space. Retaining a certain dead space is necessary to prevent anammox bacteria (AnAOB) loss under organic stress.

Homogeneous Cytochrome 579 Is an Octamer That Reacts Too Slowly With Soluble Iron to Be the Initial Iron Oxidase in the Respiratory Chain of Leptospirillum ferriphilum

The exact role that cytochrome 579 plays in the aerobic iron respiratory chain of Leptospirillum ferriphilum is unclear. This paper presents genomic, structural, and kinetic data on the cytochrome 579 purified from cell-free extracts of L. ferriphilum cultured on soluble iron. Electrospray mass spectrometry of electrophoretically homogeneous cytochrome 579 yielded two principal peaks at 16,015 and 16,141 Daltons. N-terminal amino acid sequencing of the purified protein yielded data that were used to determine the following: there are seven homologs of cytochrome 579; each homolog possesses the CXXCH heme-binding motif found in c-type cytochromes; each of the seven sequenced strains of L. ferriphilum expresses only two of the seven homologs of the cytochrome; and each homolog contains an N-terminal signal peptide that directs the mature protein to an extra-cytoplasmic location. Static light scattering and macroion mobility measurements on native cytochrome 579 yielded masses of 125 and 135 kDaltons, respectively. The reduced alkaline pyridine hemochromogen spectrum of the purified cytochrome had an alpha absorbance maximum at 567 nm, a property not exhibited by any known heme group. The iron-dependent reduction and oxidation of the octameric cytochrome exhibited positively cooperative kinetic behavior with apparent Hill coefficients of 5.0 and 3.7, respectively, when the purified protein was mixed with mM concentrations of soluble iron. Consequently, the extrapolated rates of reduction at sub-mM iron concentrations were far too slow for cytochrome 579 to be the initial iron oxidase in the aerobic respiratory chain of L. ferriphilum. Rather, these observations support the hypothesis that the acid-stable cytochrome 579 is a periplasmic conduit of electrons from initial iron oxidation in the outer membrane of this Gram-negative bacterium to a terminal oxidase in the plasma membrane.

Monitoring of bacterial community structure and growth: An alternative tool for biofilm microanalysis

Microorganisms, such as bacteria, tend to aggregate and grow on surfaces, secreting extracellular polymeric substances (EPS), forming biofilms. Biofilm formation is a life strategy, because through it microorganisms can create their own microhabitats. Whether for remediation of pollutants or application in the biomedical field, several methodological approaches are necessary for a more accurate analysis of the role and potential use of bacterial biofilms. The use of computerized microtomography to monitor biofilm growth appears to be an advantageous tool due to its non-destructive character and its ability to render 2D and 3D visualization of the samples. In this study, we used several techniques such as analysis of microbiological parameters and biopolymer concentrations to corroborate porosity quantified by 2D and 3D imaging. Quantification of the porosity of samples by microtomography was verified by increased enzymatic activity and, consequently, higher EPS biopolymer synthesis to form biofilm, indicating growth of the biofilm over 96 ​h. Our interdisciplinary approach provides a better understanding of biofilm growth, enabling integrated use of these techniques as an important tool in bioremediation studies of environments impacted by pollutants.

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Biofilm formation is a strategy by which bacteria can create their own microhabitats.

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Interdisciplinary approach provides a better understanding of biofilm growth.

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Integrated use of techniques is an important tool in bioremediation studies.

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X-ray microtomography proved to be a viable technique for monitoring biofilm growth.

Heterogeneity of the diverse aerobic sludge granules self-cultivated in a membrane bioreactor with enhanced internal circulation

The present work revealed the heterogeneity of the sludge granules formed in a membrane bioreactor with enhanced internal circulation, and also contributed to better understanding of their forming mechanisms. By continuously carrying out an experiment lasting for more than 3 months with the floc sludge from a local municipal wastewater treatment plant as inoculation sludge, diverse aerobic sludge granules were found to be successfully self-cultivated within the reactor. The results of scanning electron microscopy, fluorescence microscope and high-throughput sequencing measurement indicated that the obtained diverse granules exhibited quite obvious heterogeneity in their basic physico-chemical and microbial properties, and filamentous bacteria actually acted as a main skeleton to keep the self-cultivated sludge granules stable in both their structure and morphology. Furthermore, stable and high COD and TN removal achieved, over 85% and 60%, respectively, which confirmed its usefulness in wastewater treatment.

Biofilms: an emergent form of bacterial life

Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle.

Proteomic tools to decipher microbial community structure and functioning

Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.

Proteomics dedicated to biofilmology: What have we learned from a decade of research?

Advances in proteomics techniques over the past decade, closely integrated with genomic and physicochemical approach, have played a great role in developing knowledge of the biofilm lifestyle of bacteria. Despite bacterial proteome versatility, many studies have demonstrated the ability of proteomics approaches to elucidating the biofilm phenotype. Though these investigations have been largely used for biofilm studies in the last decades, they represent, however, a very low percentage of proteomics works performed up to now. Such approaches have offered new targets for combating microbial biofilms by providing a comprehensive quantitative and qualitative overview of their protein cell content. Herein, we summarized the state of the art in knowledge about biofilm physiology after one decade of proteomic analysis. In a second part, we highlighted missing research tracks for the next decade, emphasizing the emergence of posttranslational modifications in proteomic studies stemming from recent advances in mass spectrometry-based proteomics.

Presentation on mechanisms and applications of chalcopyrite and pyrite bioleaching in biohydrometallurgy - a presentation

This review outlines classic and current research, scientific documents and research achievements in bioleaching, particularly in respect of the bioleaching of chalcopyrite and pyrite. The diversity and commonality of the microbial leaching process can be easily studied through comparing the bioleaching mechanism and the application of these two metal sulfides. The crystal, electronic and surface structures of chalcopyrite and pyrite are summarized in detail in this paper. It determines the specific and complicated interaction pathways, kinetics of the atmospheric/aqueous oxidation, and the control process of bioleaching of the minerals as the precondition. Bioleaching of metal sulfides is performed by a diverse group of microorganisms and microbial communities. The species of the bacteria which have a significant effect on leaching ores are miraculously diverse. The newly identified acidophilic microorganisms with unique characteristics for efficient bioleaching of sulfidic minerals are increasing sharply. The cell-to-cell communication mechanisms, which are still implicit, elusive and intangible at present day, have gradually become a research hotspot. The different mineralogy characteristics and the acid solubility of the metal sulfides (e.g., chalcopyrite and pyrite) cause two different dissolution pathways, the thiosulfate and the polysulfide pathways. The bioleaching mechanisms are categorized by contact (an electrostatic attachment) and noncontact (planktonic) process, with emphasis on the produce of extracellular polymeric substances and formation of biofilm on the surface of the metal sulfides in this paper. The division of the direct and indirect effect are not adopted due to the redox chain, the reduction of the ferric iron and oxidation of the ferrous iron. The molecular oxygen is reduced by the electrons extracted from the specific metal sulfide, via a redox chain forming a supercomplex spanning the periplasmic space and connecting both outer and inner membrane. The passivation of the mineral surface can obviously hinder the dissolution of metal sulfides during the bioleaching process, which is significantly affected by the kinetic model, microenvironment on the surface of ore and the leach conditions, such as temperature, pH and Eh. The new development of mechanism research, enhanced and intensified technologies on the bioleaching of chalcopyrite and pyrite, are conducted and summarized from the different branches of natural science. Some are depicted and explained based on molecular level in this paper. Catalyst and catalytic mechanisms in bioleaching and biooxidation for this two sulfide minerals have been concluded and applied for several decades, the continuous emergence of the new material and technology are also gradually applied into the biohydrometallurgy. The industrial applications of the bioleaching on chalcopyrite and pyrite are totally based on the understanding of the interaction mechanism between microbes and minerals, the optimization of ore leaching conditions and the development of new material and the leaching equipment. It is not incredible and unimaginable to take a different bioleaching process and diagram to deal with the two sulfuric metals, which is vital to succeed in elevating the leaching rate of copper.

(15)N- and (2)H proteomic stable isotope probing links nitrogen flow to archaeal heterotrophic activity

Understanding how individual species contribute to nutrient transformations in a microbial community is critical to prediction of overall ecosystem function. We conducted microcosm experiments in which floating acid mine drainage (AMD) microbial biofilms were submerged - recapitulating the final stage in a natural biofilm life cycle. Biofilms were amended with either (15)NH4(+) or deuterium oxide ((2)H2O) and proteomic stable isotope probing (SIP) was used to track the extent to which different members of the community used these molecules in protein synthesis across anaerobic iron-reducing, aerobic iron-reducing and aerobic iron-oxidizing environments. Sulfobacillus spp. synthesized (15)N-enriched protein almost exclusively under iron-reducing conditions whereas the Leptospirillum spp. synthesized (15)N-enriched protein in all conditions. There were relatively few (15)N-enriched archaeal proteins, and all showed low atom% enrichment, consistent with Archaea synthesizing protein using the predominantly (14)N biomass derived from recycled biomolecules. In parallel experiments using (2)H2O, extensive archaeal protein synthesis was detected in all conditions. In contrast, the bacterial species showed little protein synthesis using (2)H2O. The nearly exclusive ability of Archaea to synthesize proteins using (2)H2O may be due to archaeal heterotrophy, whereby Archaea offset deleterious effects of (2)H by accessing (1)H generated by respiration of organic compounds.

Proteogenomics for environmental microbiology

Proteogenomics sensu stricto refers to the use of proteomic data to refine the annotation of genomes from model organisms. Because of the limitations of automatic annotation pipelines, a relatively high number of errors occur during the structural annotation of genes coding for proteins. Whether putative orphan sequences or short genes encoding low-molecular-weight proteins really exist is still frequently a mystery. Whether start codons are well defined is also an open debate. These problems are exacerbated for genomes of microorganisms belonging to poorly documented genera, as related sequences are not always available for homology-guided annotation. The functional annotation of a significant proportion of genes is also another well-known issue when annotating environmental microorganisms. High-throughput shotgun proteomics has recently greatly evolved, allowing the exploration of the proteome from any microorganism at an unprecedented depth. The structural and functional annotation process may be usefully complemented with experimental data. Indeed, proteogenomic mapping has been successfully performed for a wide variety of organisms. Specific approaches devoted to systematically establishing the N-termini of a large set of proteins are being developed. N-terminomics is giving rise to datasets of experimentally proven translational start codons as well as validated peptide signals for secreted proteins. By extension, combining genomic and proteomic data is becoming routine in many research projects. The proteomic analysis of organisms with unfinished genome sequences, the so-called composite proteomics, and the search for microbial biomarkers by bottom-up and top-down combined approaches are some examples of proteogenomic-flavored studies. They illustrate the advent of a new era of environmental microbiology where proteomics and genomics are intimately integrated to answer key biological questions.

Sample handling and mass spectrometry for microbial metaproteomic analyses

Metaproteomic studies of whole microbial communities from environmental samples (e.g., soil, sediments, freshwater, seawater, etc.) have rapidly increased in recent years due to many technological advances in mass spectrometry (MS). A single 24-h liquid chromatograph-tandem mass spectrometry (LC-MS/MS) measurement can potentially detect and quantify thousands of proteins from many dominant and subdominant naturally occurring microbial populations. Importantly, amino acid sequences and relative abundance information for detected peptides are determined, which allows for the characterization of expressed protein functions within communities and specific matches to be made to microbial lineages, with potential subspecies resolution. Continued optimization of protein extraction and fractionation protocols, development of quantification methods, and advances in mass spectrometry instrumentation are enabling more accurate and comprehensive peptide detection within samples, leading to wider research applicability, greater ease of use, and overall accessibility. This chapter provides a brief overview of metaproteomics experimental options, including a general protocol for sample handling and LC-MS/MS measurement.

Insight into the evolution of the iron oxidation pathways

Iron is a ubiquitous element in the universe. Ferrous iron (Fe(II)) was abundant in the primordial ocean until the oxygenation of the Earth's atmosphere led to its widespread oxidation and precipitation. This change of iron bioavailability likely put selective pressure on the evolution of life. This element is essential to most extant life forms and is an important cofactor in many redox-active proteins involved in a number of vital pathways. In addition, iron plays a central role in many environments as an energy source for some microorganisms. This review is focused on Fe(II) oxidation. The fact that the ability to oxidize Fe(II) is widely distributed in Bacteria and Archaea and in a number of quite different biotopes suggests that the dissimilatory Fe(II) oxidation is an ancient energy metabolism. Based on what is known today about Fe(II) oxidation pathways, we propose that they arose independently more than once in evolution and evolved convergently. The iron paleochemistry, the phylogeny, the physiology of the iron oxidizers, and the nature of the cofactors of the redox proteins involved in these pathways suggest a possible scenario for the timescale in which each type of Fe(II) oxidation pathways evolved. The nitrate dependent anoxic iron oxidizers are likely the most ancient iron oxidizers. We suggest that the phototrophic anoxic iron oxidizers arose in surface waters after the Archaea/Bacteria-split but before the Great Oxidation Event. The neutrophilic oxic iron oxidizers possibly appeared in microaerobic marine environments prior to the Great Oxidation Event while the acidophilic ones emerged likely after the advent of atmospheric O(2). This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

Waste gas biofiltration: advances and limitations of current approaches in microbiology

As confidence in gas biofiltration efficacy grows, ever more complex malodorant and toxic molecules are ameliorated. In parallel, for many countries, emission control legislation becomes increasingly stringent to accommodate both public health and climate change imperatives. Effective gas biofiltration in biofilters and biotrickling filters depends on three key bioreactor variables: the support medium; gas molecule solubilization; and the catabolic population. Organic and inorganic support media, singly or in combination, have been employed and their key criteria are considered by critical appraisal of one, char. Catabolic species have included fungal and bacterial monocultures and, to a lesser extent, microbial communities. In the absence of organic support medium (soil, compost, sewage sludge, etc.) inoculum provision, a targeted enrichment and isolation program must be undertaken followed, possibly, by culture efficacy improvement. Microbial community process enhancement can then be gained by comprehensive characterization of the culturable and total populations. For all species, support medium attachment is critical and this is considered prior to filtration optimization by water content, pH, temperature, loadings, and nutrients manipulation. Finally, to negate discharge of fungal spores, and/or archaeal and/or bacterial cells, capture/destruction technologies are required to enable exploitation of the mineralization product CO(2).

Metal affinity enrichment increases the range and depth of proteome identification for extracellular microbial proteins

Many key proteins, such as those involved in cellular signaling or transcription, are difficult to measure in microbial proteomic experiments due to the interfering presence of more abundant, dominant proteins. In an effort to enhance the identification of previously undetected proteins, as well as provide a methodology for selective enrichment, we evaluated and optimized immobilized metal affinity chromatography (IMAC) coupled with mass spectrometric characterization of extracellular proteins from an extremophilic microbial community. Seven different metals were tested for IMAC enrichment. The combined results added ∼20% greater proteomic depth to the extracellular proteome. Although this IMAC enrichment could not be conducted at the physiological pH of the environmental system, this approach did yield a reproducible and specific enrichment of groups of proteins with functions potentially vital to the community, thereby providing a more extensive biochemical characterization. Notably, 40 unknown proteins previously annotated as "hypothetical" were enriched and identified for the first time. Examples of identified proteins includes a predicted TonB signal sensing protein homologous to other known TonB proteins and a protein with a COXG domain previously identified in many chemolithoautotrophic microbes as having a function in the oxidation of CO.

Targeted isolation of proteins from natural microbial communities living in an extreme environment

Microorganisms from extreme environments are often very difficult to cultivate, precluding detailed study by biochemical and physiological techniques. Recent advances in genomic sequencing and proteomic measurements of samples obtained from natural communities have allowed new access to these uncultivated extremophiles and identified abundant proteins that can be isolated directly from natural samples. Here we report the isolation of two abundant heme proteins from low-diversity biofilm microbial communities that thrive in very acidic (pH ~ 1), metal-rich water in a subsurface mine. Purification and detailed characterization of these proteins has afforded new insight into the possible mechanism of Fe(II) oxidation by Leptospirillum Group II, the dominant population in most of these biofilms, and demonstrated that the abundance and posttranslational modifications of one of these proteins is dependent on the lifecycle of the biofilm.