Survival strategies of bacteria in the natural environment

Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis

Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolyzing urea, and play an important role in marine nitrogen cycle. However, there is still an incomplete understanding of UPB and their ecological functions in the cultivation environment of the red macroalgae Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. A total of 34 isolates belonging to four main bacterial phyla i.e. (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains contained urease. All of these UPB exhibited different urease activities, which were determined by the Berthelot reaction colorimetry assay. Additionally, the UPB strain (G13) isolated from G. lemaneiformis with higher urease activity was selected for co-culture with G. lemaneiformis to explore its role in promoting or inhibiting nitrogen uptake by macroalgae. The results showed a significant increase in urea consumption in the culture medium and the total cellular nitrogen in G. lemaneiformis in the UPB-co culture group compared to the sterile group. This suggests that the selected UPB strain positively influences nitrogen uptake by G. lemaneiformis. Similarly, isotopic assays revealed that the δ15N content of G. lemaneiformis was significantly higher in the UPB-co culture than in the control group, where δ15N-urea was the only nitrogen source in the culture medium. This indicates that the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of δ15N was found in G. lemaneiformis with epiphytic bacteria compared to sterilized (i.e. control), showing that epiphytic bacteria, along with UPB, have a compound effect in helping G. lemaneiformis absorb more nitrogen from urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be an important player in marine nitrogen cycling.

Active and dormant microorganisms on glacier surfaces

Glacier and ice sheet surfaces host diverse communities of microorganisms whose activity (or inactivity) influences biogeochemical cycles and ice melting. Supraglacial microbes endure various environmental extremes including resource scarcity, frequent temperature fluctuations above and below the freezing point of water, and high UV irradiance during summer followed by months of total darkness during winter. One strategy that enables microbial life to persist through environmental extremes is dormancy, which despite being prevalent among microbial communities in natural settings, has not been directly measured and quantified in glacier surface ecosystems. Here, we use a combination of metabarcoding and metatranscriptomic analyses, as well as cell-specific activity (BONCAT) incubations to assess the diversity and activity of microbial communities from glacial surfaces in Iceland and Greenland. We also present a new ecological model for glacier microorganisms and simulate physiological state-changes in the glacial microbial community under idealized (i) freezing, (ii) thawing, and (iii) freeze-thaw conditions. We show that a high proportion (>50%) of bacterial cells are translationally active in-situ on snow and ice surfaces, with Actinomycetota, Pseudomonadota, and Planctomycetota dominating the total and active community compositions, and that glacier microorganisms, even when frozen, could resume translational activity within 24 h after thawing. Our data suggest that glacial microorganisms respond rapidly to dynamic and changing conditions typical of their natural environment. We deduce that the biology and biogeochemistry of glacier surfaces are shaped by processes occurring over short (i.e., daily) timescales, and thus are susceptible to change following the expected alterations to the melt-regime of glaciers driven by climate change. A better understanding of the activity of microorganisms on glacier surfaces is critical in addressing the growing concern of climate change in Polar regions, as well as for their use as analogues to life in potentially habitable icy worlds.

PCR-based detection of pathogens in improved water sources: a scoping review protocol of the evidence in low-income and middle-income countries

INTRODUCTION

Occurrence of diverse human enteric bacterial, viral and protozoal pathogens in improved drinking water because of pathogenic microbial contamination is of increasing public health concern, particularly in low-income and middle-income countries (LMICs). Detecting microbial pathogens in water supplies comprehensively and accurately is beneficial to ensure the safety of water in LMICs where water contamination is a major concern. Application of PCR-based methods in detecting the microbial quality of water provides more accurate, sensitive and rapid outcomes over conventional methods of microbial identification and quantification. Therefore, exploring water quality outcomes generated through PCR-based methods is important to better understand the status and monitor progress towards internationally set goals for LMICs. This scoping review aims to map the existing evidence on the magnitude and characteristics of diarrhoeagenic pathogens as detected by PCR-based methods in improved water sources within the context of LMICs.

METHODS AND ANALYSIS

This study will be undertaken in line with the Joanna Briggs Institute (JBI) methodology for scoping reviews. We will consider the available publications covering PCR-based microbial water quality assessment of improved drinking water sources in LMICs. Searches will be undertaken in PubMed/Medline, Scopus, Web of Science, JBI, Cochrane Library and Google Scholar. A grey literature search will be conducted in Google and ProQuest.

ETHICS AND DISSEMINATION

The College of Natural and Computational Science Institution Review Board of Addis Ababa University gave formal ethical approval to this study protocol. The findings of this study will be disseminated to the concerned body through peer-reviewed publications, presentations and summaries.

Suboptimal resource allocation in changing environments constrains response and growth in bacteria

To respond to fluctuating conditions, microbes typically need to synthesize novel proteins. As this synthesis relies on sufficient biosynthetic precursors, microbes must devise effective response strategies to manage depleting precursors. To better understand these strategies, we investigate the active response of Escherichia coli to changes in nutrient conditions, connecting transient gene expression to growth phenotypes. By synthetically modifying gene expression during changing conditions, we show how the competition by genes for the limited protein synthesis capacity constrains cellular response. Despite this constraint cells substantially express genes that are not required, trapping them in states where precursor levels are low and the genes needed to replenish the precursors are outcompeted. Contrary to common modeling assumptions, our findings highlight that cells do not optimize growth under changing environments but rather exhibit hardwired response strategies that may have evolved to promote fitness in their native environment. The constraint and the suboptimality of the cellular response uncovered provide a conceptual framework relevant for many research applications, from the prediction of evolution to the improvement of gene circuits in biotechnology.

In vitro antibacterial and antibiofilm effects of cold atmospheric microwave plasma against Pseudomonas aeruginosa causing canine skin and ear infections

BACKGROUND

Pseudomonas aeruginosa is an opportunist pathogen that causes purulent inflammation in the skin and in the ears of dogs. Among the various virulence factors of P. aeruginosa, biofilms have been reported to result in antibiotic resistance, leading to therapeutic limitations. Cold atmospheric microwave plasma (CAMP) is known to have a high antimicrobial effect, which causes physical cell wall rupture and DNA damage.

HYPOTHESIS/OBJECTIVES

The objective of this study was to evaluate the antibacterial and antibiofilm effects of CAMP against planktonic bacteria and the biofilm of P. aeruginosa.

METHODS AND MATERIALS

The antibacterial effect of CAMP against P. aeruginosa ATCC10145 and clinical isolates (n = 30) was evaluated using the colony count method. We also assessed the effect of CAMP on biofilm of P. aeruginosa ATCC strain by the colony count method, water-soluble tetrazolium salt (WST) assay and confocal laser scanning microscopy (CLSM).

RESULTS

The complete eradication of P. aeruginosa (ATCC strain and clinical isolates) was achieved within 120 s at 50 W, and clinical isolates required 60 s shorter than the ATCC strain for complete eradication at 50 W. We also confirmed the time-dependent bactericidal effect of CAMP at 50 W against ATCC strain biofilm.

CONCLUSIONS AND CLINICAL IMPORTANCE

CAMP was effective against both planktonic bacteria and biofilm formation of P. aeruginosa. However, further studies on in vivo efficacy and safety in canine skin and ears are necessary to fully validate its clinical application.

Treatment of municipal wastewater by employing membrane bioreactors combined with efficient nitration microbial communities isolated by Isolation Chip with Plate Streaking technology

In this research, we developed a method so-called Isolation Chip with Plate Streaking (ICPS) to selectively enrich nitrifying microbial consortium for treating municipal wastewater. In batch experiment, these bacterial communities were able to remove NH₃ -N in 72 h with an efficiency of 96%. Firmicutes, Bacteroidetes, and Proteobacteria species are dominant bacteria in these communities. When the bacterial communities were used in the membrane bioreactor under typical condition, the removal efficiency was 81.0%. In contrast, under the actual wastewater condition, the efficiency could reach 91.2%. All above results showed clearly that the consortium selected by our ICPS method could achieve high-efficient NH₃ -N removal, thus offering a reliable technique for screening functional microorganisms in the field of water treatment. PRACTITIONER POINTS: ICPS technology was designed and used for screening specialized NH₃ -N-removing isolates. The screening process benefited the growth of the dominant nitrifying bacteria Firmicutes and Bacteroidetes. When the functional bacteria applied into the MBR, the NH₃ -N removal efficiency was 91.2% under actual wastewater conditions.

Metal-Organic Frameworks as a Versatile Materials Platform for Unlocking New Potentials in Biocatalysis

Biocatalysts immobilization with nanomaterials has promoted the development of biocatalysis significantly and made it an indispensable part of catalysis industries nowadays. Metal-organic frameworks (MOFs), constructed from organic linkers and metal ions or clusters, have raised significant interests for biocatalysts immobilization in recent years. The diversity of building units, molecular-scale tunability, and modular synthetic routes of MOFs greatly expand its ability as the host to integrate with biocatalysts. In this review, the general synthetic strategies of MOFs with biocatalysts are first summarized. Then, the recent progress of MOFs as a versatile host for a series of biocatalysts, including natural enzymes, nanozymes, and organism-based biocatalysts, followed by the introduction of MOFs themselves as biocatalysts, is discussed. Furthermore, the stimuli-responsive properties of MOFs themselves or the additional functionalization of protein, polymer, and peptide within/on MOF that enable the biocatalysts with the controllable and tunable behavior are also summarized, which could unlock new potentials in biocatalysis. Finally, a perspective of the upcoming challenges, potential impacts, and future directions of biocatalytic MOFs is provided.

Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara

BACKGROUND

Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening for antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study desert Streptomyces microbiology and ecology from a genomic perspective.

RESULTS

Strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequencing as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed using Pacific Biosciences Sequel II technology (PacBio), which showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified protein coding genes was 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17. Although the strains have different phenotypes and are from different regions, they showed very high similarities at the DNA level. The two strains are more similar to each other than either is to the closest database strain. The search for potential secondary metabolites was performed using antiSMASH and predicted 29 biosynthetic gene clusters (BGCs). Several BGCs and proteins were related to the biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity.

CONCLUSION

The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information provides tools to study ecological adaptation in a desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first to be sequenced for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to more profoundly explore the desert microbiome.

Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils

Candidatus Dormibacterota is an uncultured bacterial phylum found predominantly in soil that is present in high abundances within cold desert soils. Here, we interrogate nine metagenome-assembled genomes (MAGs), including six new MAGs derived from soil metagenomes obtained from two eastern Antarctic sites. Phylogenomic and taxonomic analyses revealed these MAGs represent four genera and five species, representing two order-level clades within Ca. Dormibacterota. Metabolic reconstructions of these MAGs revealed the potential for aerobic metabolism, and versatile adaptations enabling persistence in the 'extreme' Antarctic environment. Primary amongst these adaptations were abilities to scavenge atmospheric H₂ and CO as energy sources, as well as using the energy derived from H₂ oxidation to fix atmospheric CO₂ via the Calvin-Bassham-Benson cycle, using a RuBisCO type IE. We propose that these allow Ca. Dormibacterota to persist using H₂ oxidation and grow using atmospheric chemosynthesis in terrestrial Antarctica. Fluorescence in situ hybridization revealed Ca. Dormibacterota to be coccoid cells, 0.3-1.4 μm in diameter, with some cells exhibiting the potential for a symbiotic or syntrophic lifestyle.

Indoor Microbial Exposures and Chronic Lung Disease: From Microbial Toxins to the Microbiome

Effects of environmental microbial exposures on human health have long been of interest. Microbes were historically assumed to be harmful, but data have suggested that microbial exposures can modulate the immune system. We focus on the effects of indoor environmental microbial exposure on chronic lung diseases. We found contradictory data in bacterial studies using endotoxin as a surrogate for bacterial exposure. Contradictory data also exist in studies of fungal exposure. Many factors may modulate the effect of environmental microbial exposures on lung health, including coexposures. Future studies need to clarify which method of assessing environmental microbial exposures is most relevant.

Life on the Rocks: First Insights Into the Microbiota of the Threatened Aquatic Rheophyte Hanseniella heterophylla

Little is known about microbial communities of aquatic plants despite their crucial ecosystem function in aquatic ecosystems. Here, we analyzed the microbiota of an aquatic rheophyte, Hanseniella heterophylla, growing at three areas differing in their degree of anthropogenic disturbance in Thailand employing a metabarcoding approach. Our results show that diverse taxonomic and functional groups of microbes colonize H. heterophylla. Proteobacteria, Actinobacteria, Dothideomycetes, and Sordariomycetes form the backbone of the microbiota. Surprisingly, the beneficial microbes reported from plant microbiomes in terrestrial habitats, such as N-fixing bacteria and ectomycorrhizal fungi, were also frequently detected. We showed that biofilms for attachment of H. heterophylla plants to rocks may associate with diverse cyanobacteria (distributed in eight families, including Chroococcidiopsaceae, Coleofasciculaceae, Leptolyngbyaceae, Microcystaceae, Nostocaceae, Phormidiaceae, Synechococcaceae, and Xenococcaceae) and other rock biofilm-forming bacteria (mainly Acinetobacter, Pseudomonas, and Flavobacterium). We found distinct community compositions of both bacteria and fungi at high and low anthropogenic disturbance levels regardless of the study areas. In the highly disturbed area, we found strong enrichment of Gammaproteobacteria and Tremellomycetes coupled with significant decline of total bacterial OTU richness. Bacteria involved with sulfamethoxazole (antibiotic) degradation and human pathogenic fungi (Candida, Cryptococcus, Trichosporon, and Rhodotorula) were exclusively detected as indicator microorganisms in H. heterophylla microbiota growing in a highly disturbed area, which can pose a major threat to human health. We conclude that aquatic plant microbiota are sensitive to anthropogenic disturbance. Our results also unravel the potential use of this plant as biological indicators in remediation or treatment of such disturbed ecosystems.

Loop-mediated isothermal amplification: Development, validation and application of simple and rapid assays for quantitative detection of species of Arcobacteraceae family- and species-specific Aliarcobacter faecis and Aliarcobacter lanthieri

Aim

The family Arcobacteraceae formerly genus Arcobacter has recently been reclassified into six genera. Among nine species of the genus Aliarcobacter, Aliarcobacter faecis and Aliarcobacter lanthieri have been identified as emerging pathogens potentially cause health risks to humans and animals. This study was designed to develop/optimize, validate and apply Arcobacteraceae family‐ and two species‐specific (A. faecis and A. lanthieri) loop‐mediated isothermal amplification (LAMP) assays to rapidly detect and quantify total number of cells in various environmental niches.

Methods and Results

Three sets of LAMP primers were designed from conserved and variable regions of 16S rRNA (family‐specific) and gyrB (species‐specific) genes. Optimized Arcobacteraceae family‐specific LAMP assay correctly amplified and detected 24 species, whereas species‐specific LAMP assays detected A. faecis and A. lanthieri reference strains as well as 91 pure and mixed culture isolates recovered from aquatic and faecal sources. The specificity of LAMP amplification of A. faecis and A. lanthieri was further confirmed by restriction fragment length polymorphism analysis. Assay sensitivities were tested using variable DNA concentrations extracted from simulated target species cells in an autoclaved agricultural water sample by achieving a minimum detection limit of 10 cells mL⁻¹ (10 fg). Direct DNA‐based quantitative detection, from agricultural surface water, identified A. faecis (17%) and A. lanthieri (1%) at a low frequency compared to family‐level (93%) with the concentration ranging from 2·1 × 10¹ to 2·2 × 10⁵ cells 100 mL⁻¹.

Conclusions

Overall, these three DNA‐based rapid and cost‐effective novel LAMP assays are sensitive and can be completed in less than 40 min. They have potential for on‐site quantitative detection of species of family Arcobacteraceae, A. faecis and A. lanthieri in food, environmental and clinical matrices.

Significance and Impact of the Study

The newly developed LAMP assays are specific, sensitive, accurate with higher reproducibility that have potential to facilitate in a less equipped lab setting and can help in early quantitative detection and rate of prevalence in environmental niches. The assays can be adopted in the diagnostic labs and epidemiological studies.

Time-of-day-dependent responses of cyanobacterial cellular viability against oxidative stress

As an adaptation to periodic fluctuations of environmental light, photosynthetic organisms have evolved a circadian clock. Control by the circadian clock of many cellular physiological functions, including antioxidant enzymes, metabolism and the cell cycle, has attracted attention in the context of oxidative stress tolerance. However, since each physiological function works in an integrated manner to deal with oxidative stress, whether or not cell responses to oxidative stress are under circadian control remains an open question. In fact, circadian rhythms of oxidative stress tolerance have not yet been experimentally demonstrated. In the present work, we applied an assay using methyl viologen (MV), which generates reactive oxygen species (ROS) under light irradiation, and experimentally verified the circadian rhythms of oxidative stress tolerance in photosynthetic cells of the cyanobacterium Synechococcus elongatus PCC 7942, a standard model species for investigation of the circadian clock. Here, we report that ROS generated by MV treatment causes damage to stroma components and not to the photosynthetic electron transportation chain, leading to reduced cell viability. The degree of decrease in cell viability was dependent on the subjective time at which oxidative stress was applied. Thus, oxidative stress tolerance was shown to exhibit circadian rhythms. In addition, the rhythmic pattern of oxidative stress tolerance disappeared in mutant cells lacking the essential clock genes. Notably, ROS levels changed periodically, independent of the MV treatment. Thus, we demonstrate for the first time that in cyanobacterial cells, oxidative stress tolerance shows circadian oscillation.

Tenacity of Enterococcus cecorum at different environmental conditions

AIMS

Our aim was to analyse the survival of Enterococcus cecorum (EC) at various temperatures, relative air humidities and on different substrates commonly existing in broiler houses.

METHODS AND RESULTS

A pathogenic EC isolate (EC14) was used to inoculate sterile litter, polyvinyl chloride (PVC) and dust samples. Incubation at 37, 25 or 15°C with either 32% relative humidity (RH) or 78% RH followed. At defined time points (0-4272 h post-inoculation), samples were examined in triplicate for the total viable count. Selected combinations were repeated for a non-pathogenic and two additional pathogenic EC strains. For EC14, the measured survival time ranged from 48 to 4272 h (178 days) depending on the substrate-humidity-temperature combination. The longevity was the highest on litter, followed by dust and then PVC. Lower temperatures facilitated its survival, lower relative air humidity favoured the survival only in combination with 25 or 15°C. All three pathogenic strains showed longer survival times (up to 432 h, 18 days) compared to the non-pathogenic EC strain (168 h, 7 days) under the same conditions.

CONCLUSIONS

Enterococcus cecorum demonstrates a high persistence in the environment especially at 15°C and 32% RH.

SIGNIFICANCE AND IMPACT OF THE STUDY

Hygiene management plans should consider the durability of EC and the risk of a carry-over to control consecutive EC outbreaks.

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.

Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth

Bacterial growth under nutrient-rich and starvation conditions is intrinsically tied to the environmental history and physiological state of the population. While high-throughput technologies have enabled rapid analyses of mutant libraries, technical and biological challenges complicate data collection and interpretation. Here, we present a framework for the execution and analysis of growth measurements with improved accuracy over that of standard approaches. Using this framework, we demonstrate key biological insights that emerge from consideration of culturing conditions and history. We determined that quantification of the background absorbance in each well of a multiwell plate is critical for accurate measurements of maximal growth rate. Using mathematical modeling, we demonstrated that maximal growth rate is dependent on initial cell density, which distorts comparisons across strains with variable lag properties. We established a multiple-passage protocol that alleviates the substantial effects of glycerol on growth in carbon-poor media, and we tracked growth rate-mediated fitness increases observed during a long-term evolution of Escherichia coli in low glucose concentrations. Finally, we showed that growth of Bacillus subtilis in the presence of glycerol induces a long lag in the next passage due to inhibition of a large fraction of the population. Transposon mutagenesis linked this phenotype to the incorporation of glycerol into lipoteichoic acids, revealing a new role for these envelope components in resuming growth after starvation. Together, our investigations underscore the complex physiology of bacteria during bulk passaging and the importance of robust strategies to understand and quantify growth.IMPORTANCE How starved bacteria adapt and multiply under replete nutrient conditions is intimately linked to their history of previous growth, their physiological state, and the surrounding environment. While automated equipment has enabled high-throughput growth measurements, data interpretation and knowledge gaps regarding the determinants of growth kinetics complicate comparisons between strains. Here, we present a framework for growth measurements that improves accuracy and attenuates the effects of growth history. We determined that background absorbance quantification and multiple passaging cycles allow for accurate growth rate measurements even in carbon-poor media, which we used to reveal growth-rate increases during long-term laboratory evolution of Escherichia coli Using mathematical modeling, we showed that maximum growth rate depends on initial cell density. Finally, we demonstrated that growth of Bacillus subtilis with glycerol inhibits the future growth of most of the population, due to lipoteichoic acid synthesis. These studies highlight the challenges of accurate quantification of bacterial growth behaviors.

Atmospheric Biodetection Part I: Study of Airborne Bacterial Concentrations from January 2018 to May 2020 at Saclay, France

Background: The monitoring of bioaerosol concentrations in the air is a relevant endeavor due to potential health risks associated with exposure to such particles and in the understanding of their role in climate. In this context, the atmospheric concentrations of bacteria were measured from January 2018 to May 2020 at Saclay, France. The aim of the study was to understand the seasonality, the daily variability, and to identify the geographical origin of airborne bacteria. Methods: 880 samples were collected daily on polycarbonate filters, extracted with purified water, and analyzed using the cultivable method and flow cytometry. A source receptor model was used to identify the origin of bacteria. Results: A tri-modal seasonality was identified with the highest concentrations early in spring and over the summer season with the lowest during the winter season. Extreme changes occurred daily due to rapid changes in meteorological conditions and shifts from clean air masses to polluted ones. Conclusion: Our work points toward bacterial concentrations originating from specific seasonal-geographical ecosystems. During pollution events, bacteria appear to rise from dense urban areas or are transported long distances from their sources. This key finding should drive future actions to better control the dispersion of potential pathogens in the air, like persistent microorganisms originating from contaminated areas.

Use of an Artificial Miniaturized Enzyme in Hydrogen Peroxide Detection by Chemiluminescence

Advanced oxidation processes represent a viable alternative in water reclamation for potable reuse. Sensing methods of hydrogen peroxide are, therefore, needed to test both process progress and final quality of the produced water. Several bio-based assays have been developed so far, mainly relying on peroxidase enzymes, which have the advantage of being fast, efficient, reusable, and environmentally safe. However, their production/purification and, most of all, batch-to-batch consistency may inherently prevent their standardization. Here, we provide evidence that a synthetic de novo miniaturized designed heme-enzyme, namely Mimochrome VI*a, can be proficiently used in hydrogen peroxide assays. Furthermore, a fast and automated assay has been developed by using a lab-bench microplate reader. Under the best working conditions, the assay showed a linear response in the 10.0-120 μM range, together with a second linearity range between 120 and 500 μM for higher hydrogen peroxide concentrations. The detection limit was 4.6 μM and quantitation limits for the two datasets were 15.5 and 186 μM, respectively. In perspective, Mimochrome VI*a could be used as an active biological sensing unit in different sensor configurations.

Perspectives on Cultivation Strategies of Archaea

Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.

Narrative of a versatile and adept species Pseudomonas putida

Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.

Nanoscale Phenotypic Textures of Yersinia pestis Across Environmentally-Relevant Matrices

The persistence of bacterial pathogens within environmental matrices plays an important role in the epidemiology of diseases, as well as impacts biosurveillance strategies. However, the adaptation potentials, mechanisms for survival, and ecological interactions of pathogenic bacteria such as Yersinia pestis are largely uncharacterized owing to the difficulty of profiling their phenotypic signatures. In this report, we describe studies on Y. pestis organisms cultured within soil matrices, which are among the most important reservoirs for their propagation. Morphological (nanoscale) and phenotypic analysis are presented at the single cell level conducted using Atomic Force Microscopy (AFM), coupled with biochemical profiles of bulk populations using Fatty Acid Methyl Ester Profiling (FAME). These studies are facilitated by a novel, customizable, 3D printed diffusion chamber that allows for control of the external environment and easy harvesting of cells. The results show that incubation within soil matrices lead to reduction of cell size and an increase in surface hydrophobicity. FAME profiles indicate shifts in unsaturated fatty acid compositions, while other fatty acid components of the phospholipid membrane or surface lipids remained consistent across culturing conditions, suggesting that phenotypic shifts may be driven by non-lipid components of Y. pestis.

Quantitative and Fast Sterility Assurance Testing of Surfaces by Enumeration of Germinable Endospores

A fast Endospore Germinability Assay (EGA) was validated with traditional plate counts to enumerate single endospore germination events for monitoring surface sterilization. The assay is based on a time-gated luminescence microscopy technique enabling visualization and enumeration of individual germinating endospores. Germinating endospores release calcium dipicolinate to form highly luminescent terbium dipicolinate complexes surrounding each germinating endospore. EGA and heterotrophic plate counting (HPC) were used to evaluate the swab/rinse recovery efficiency of endospores from stainless steel surfaces. EGA and HPC results were highly correlated for endospore recovery from stainless steel coupons inoculated with range of 1,000 endospores per coupon down to sterility. Dosage-dependent decrease of surface endospore germinability were observed in dry heat, UV irradiation, oxygen plasma and vaporized hydrogen peroxide treatments, measured with EGA and HPC. EGA is a fast and complementary method to traditional HPC for quantitative sterility assurance testing of surfaces. This work introduces and validates a 15-minute or faster assay for germinable endospores to complement the conventional lengthy, culture-based surface sterility validation, which is critical in hospitals, food and pharmaceutical industries to help minimize nosocomial infection, food spoilage, and pharmaceutical contamination.

Diversity and function of the microbial community under strong selective pressure of rotifers

We unearthed some interesting microecological discoveries while selecting for the most beneficial bacterial strains to be used as probiotics in Lecane inermis rotifer mass culture. For 3 years, we maintained the cultures of L. inermis, with selection for the highest growth rate and resistance to potential contamination. Then, we conducted further selection and isolation in two groups: rotifers inoculated with the bacterial consortium isolated from the rotifer cultures, and rotifers fed with a commercial bioproduct. Selection was conducted in demanding conditions, with particulate matter suspended in spring water as a substrate, without aeration and under strong consumer pressure, and led to selection of two cultivable strains isolated from the optimal rotifers culture. According to molecular analysis, these strains were Aeromonas veronii and Pseudomonas mosselii. Biolog® ECO plate tests showed that both investigated bacterial communities metabolized wide but similar range of substrates. Therefore, intensely selective conditions led to considerable reduction in bacterial community regarding taxonomy, but not in metabolic activity, showing a functional composition decoupling. Aside from this result, our novel selection method dedicated to the sustainable culture of two trophic levels, a directed selection procedure (DSC), could potentially lead to the development of biotechnologically valuable strains with high metabolic activity and the ability to metabolize different sorts of substrate without harmful impact on higher trophic levels.

Persistence of fecal indicator bacteria associated with zooplankton in a tropical estuary-west coast of India

In a study carried out during 2014, bacteria associated with zooplankton in the Zuari estuary were three to four orders of magnitude higher in abundance than in seawater. The live zooplankton carried much more bacterial load compared with the carcasses, and the fecal pellets harbored the highest density of bacteria, i.e., 8 × 10¹³ CFU cm^-3. The diversity of bacteria was higher in live zooplankton and also in seawater. But the activity of the zooplankton-associated bacteria was much higher compared with the free-living ones. Most of the associated bacteria belonged to the genus Enterobacter, Pseudomonas, Aeromonas, and Bacillus. In growth experiments, Aeromonas and Bacillus were found to have lower salinity optima than Enterobacter (20 psu) and Vibrio and Pseudomonas (normal seawater salinity). Better growth of bacteria was observed in the medium containing the diatom Chaetoceros sp. than Navicula sp. Bacterial isolates were also able to survive in oligotrophic conditions and produce optimum biomass in 2 days at salinity 5 psu, but in freshwater, the bacteria took a week's time to attain the optima. At salinities 0-35, the bacteria survived even for 3 months without nutrient addition, indicating resilience in these bacteria and mechanisms to persist in the estuaries even in adverse conditions.

Differential decay and prediction of persistence of Enterococcus spp. and Escherichia coli culturable cells and molecular markers in freshwater and seawater environments

To quantify the impact of fecal pollution on the microbiological bathing water quality, predictive modeling is being increasingly used in which the decay rate of the fecal indicators plays an important role. The decay of sewage-sourced enterococci and Escherichia coli culturable cells and their associated molecular markers (16SrRNA) quantified by Quantitative Reverse transcription PCR were measured in controlled microcosms as well in in situ conditions using different water types, from marine waters to fresh waters with intermediate salinity. All bacterial decays were fitted to a first order decay model. In the laboratory study, the light radiation was the most influent factor affecting E. coli and enterococci survival by culture methods although environmental conditions weakly impacted the decay of molecular markers. The results also indicated differential persistence of genetic markers and culturable organisms of fecal indicator bacteria in different water systems. For each bacteria indicator and analytical method, four equations were obtained to predict the time required to have a 90% reduction (T90) according irradiance, salinity and temperature parameters. The weighted model RMSE (Root Mean Square Error) calculated for all field experiments showed that quantification obtained with the equations defined by laboratory-based study compared reasonably well with in-situ observed quantification (0.4 and 0.2 log by standard culture methods for E. coli and Enterococcus spp. and 0.6 and 0.3 log by RT-qPCR for E. coli and Enterococcus spp. respectively). The modeling tool can be used to predict the presence of fecal pollution in marine and fresh waters in combination with either culture based- or rapid molecular methods.

Structure elucidation and proposed de novo synthesis of an unusual mono-rhamnolipid by Pseudomonas guguanensis from Chennai Port area

In this paper, we describe the isolation of an unusual type of high molecular weight monorhamnolipid attached to esters of palmitic, stearic, hexa and octadecanoic acids as against the routinely reported di-rhamnolipids linked to hydroxydecanoic acids. The bioemulsifier was column-purified and the chemical nature of the compound was elucidated using FT-IR, GC-MS and 1D [¹H and¹³C] and 2D NMR. This monorhamnolipid is extracted from a bacterium, Pseudomonas guganensis and is not reported to have biological activities, let alone emulsification abilities. The bacterium continually produced rhamnolipids when nourished with n-hexadecane as its lone carbon source. The extracellularly secreted monorhamnolipids are capable of degrading hydrocarbons, with most preference to n-hexadecane [EI₂₄ of 56 ± 1.42% by 2 mL of the spent medium]. Whilst the crude ethyl acetate partitioned extract had an EI₂₄ of 65 ± 1.43%; the purified rhamnolipid product showed 78 ± 1.75% both at 12.5 mg/mL concentration. The used-up n-hexadecane is biotransformed to prepare its own rhamnolipids which in return is utilized to degrade n-alkanes thus creating a circular pathway which is proposed herein. This bacterium can be seen as a new source of bioemulsifier to reduce hydrocarbon in polluted waters.

Optimization of microorganism preservation conditions for the development of an acute toxicity bioassay for biocides

Biocides, also referred to as 'microbicides' or 'inhibitors', are widely used in industrial processes (e.g. utility water in cooling towers) to control and/or eliminate the growth of microorganisms. Because of their inherent toxicity, their presence in various sources (e.g. river sediments, potable water) can negatively affect ecosystems. Currently available biocide detection techniques are not suitable for 'point-of-use' applications since they are tedious, complicated, and often require experienced personnel to operate. To address this concern, we sought to develop a simple-to-use toxicity bioassay based on a model microorganism (E. coli) after short (<30 min) exposure to known biocides that can be stored at room temperature (preferably) or in the fridge. Based on recent work and our expertise in polymer-based preservation of biomolecules, we leveraged this knowledge to improve E. coli preservation for biocide detection purposes. A design-of-experiments strategy was used to evaluate 16 different preservation conditions from 5 process parameters (i.e. 2^5-1 fractional factorial). It was found that pullulan, a sugar-based polymer, improved E. coli culturability by an order of magnitude after three months of storage. Also, it was found that storing E. coli in the fridge in Milli-Q water was favorable for maintaining a high level of culturability. Finally, the toxicity of three common biocides (Cetyltrimethylammonium bromide (CTAB), ProClin™ 300, and Grotan^® BK) was evaluated using a fluorescence-based assay across all 16 preservation conditions. The response of the preserved E. coli was biocide specific and at certain conditions did not vary during the entire three-month storage period.

Identification, Growth Profile and Probiotic Properties of Autochthonous Intestinal Bacteria of Sagor catfish (Hexanematichthys sagor)

　The prevalence of antibiotic resistant bacteria in aquaculture has reached alarming proportions and intensified the search for microbe derived antimicrobial compounds. This study isolated bacteria from the intestine of Sagor catfish (Hexanematichthys sagor) and screened it for antagonistic properties. Five out of 334 bacterial isolates inhibited growth of fish pathogens. The 5 bacterial strains included relatives of Shewanella haliotis, Myroides odoratimimus, Vibrio harveyi, Vibrio alginolyticus and Alcaligenes faecalis. The growth profiles and probiotic properties of these bacteria were examined. The results showed that the isolate 9 (3) 7.5.2.1, whose closest relative was S. haliotis exhibited growth and probiotic advantage compared to the other bacterial strains, such as highest doubling time and the ability to survive at all experimental temperatures (18 to 60℃) , and bile concentrations (0.01 to 1.00%) and pH (pH2 to 9) . While the bacteria with probiotic properties were successfully isolated. Further study is necessary to examine the efficiency of the probiotic candidate bacteria in boosting fish immunity against pathogens.

Imaging Macrophage Phagocytosis Using AIE Luminogen-Labeled E. coli

Phagocytosis of bacteria is an important biological process. Gaining insight into this process may greatly benefit related pathological studies and further contribute to development of therapies for infectious diseases. Tools for studying these internalization processes, however, are limited. Herein, we demonstrate the feasibility of employing an environmentally sensitive aggregation-induced emission (AIE) probe for bacteria labeling and imaging. By tracking the fluorescence variation of the stained bacteria, the pH changes of its microenvironment can be monitored. In this way, the phagocytic entry of these bacteria into the macrophage cells and the intravacuolar acidification can be visualized in real-time.

Interactions within the microbiome alter microbial interactions with host chemical defences and affect disease in a marine holobiont

Our understanding of diseases has been transformed by the realisation that people are holobionts, comprised of a host and its associated microbiome(s). Disease can also have devastating effects on populations of marine organisms, including dominant habitat formers such as seaweed holobionts. However, we know very little about how interactions between microorganisms within microbiomes - of humans or marine organisms – affect host health and there is no underpinning theoretical framework for exploring this. We applied ecological models of succession to bacterial communities to understand how interactions within a seaweed microbiome affect the host. We observed succession of surface microbiomes on the red seaweed Delisea pulchra in situ, following a disturbance, with communities ‘recovering’ to resemble undisturbed states after only 12 days. Further, if this recovery was perturbed, a bleaching disease previously described for this seaweed developed. Early successional strains of bacteria protected the host from colonisation by a pathogenic, later successional strain. Host chemical defences also prevented disease, such that within-microbiome interactions were most important when the host’s chemical defences were inhibited. This is the first experimental evidence that interactions within microbiomes have important implications for host health and disease in a dominant marine habitat-forming organism.

Regrowth-delay body as a bacterial subcellular structure marking multidrug-tolerant persisters

Bacteria have long been recognized to be capable of entering a phenotypically non-growing persister state, in which the cells exhibit an extended regrowth lag and a multidrug tolerance, thus posing a great challenge in treating infectious diseases. Owing to their non-inheritability, low abundance of existence, lack of metabolic activities, and high heterogeneity, properties of persisters remain poorly understood. Here, we report our accidental discovery of a subcellular structure that we term the regrowth-delay body, which is formed only in non-growing bacterial cells and sequesters multiple key proteins. This structure, that dissolves when the cell resumes growth, is able to be viewed as a marker of persisters. Our studies also indicate that persisters exhibit different depth of persistence, as determined by the status of their regrowth-delay bodies. Our findings imply that suppressing the formation and/or promoting the dissolution of regrowth-delay bodies could be viable strategies for eradicating persisters.

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.

Non-targeted metabolomics unravels a media-dependent prodiginines production pathway in Streptomyces coelicolor A3(2)

The genus Streptomyces is the best-known source of therapeutic secondary metabolites, especially antibiotics with pharmaceutical applications. Here, we performed a comparative study based on the time-resolved metabolic disparity in S. coelicolor A3(2) subjected to fermentative cultivation in two different types of media (R2YE and RSM3) in order to investigate secondary metabolite production pathways. The relative abundance of secondary metabolites, such as prodiginines, indoles, germicidins, and selected diketopiperazines, was increased in S. coelicolor A3(2) cultivated in R2YE medium compared to that in RSM3 medium, variably at the late-log and stationary phases of fermentative growth. Correlation analysis indicated that “antibiotic prodiginines” contributed maximally to the absorption maxima (A₅₃₀) of culture supernatants, indicating their optimal production at 96 hours in R2YE medium. A higher abundance of L-proline (48–72 hours) followed by prodiginines (96 hours) was evident, substantiating the intertwined links between precursor and activated prodiginines pathway. Similarly, the higher abundance of indoles was concurrent with tryptophan levels in the shikimate pathway, whereas diketopiperazines were synchronously abundant along with the levels of phenylalanine, leucine, and proline. Additionally, acetyl-CoA induced the acetate pathway, resulting in the production of germicidins. Thus, our results demonstrate that S. coelicolor A3(2) produces specific secondary metabolites by enhancing the dedicated metabolic pathway responsible for their production. In conclusion, our results from this study provide insight into the metabolic pathways of S. coelicolor A3(2), and can be applied to further optimize the production of prodiginines.

Responses of soil microbial communities to nutrient limitation in the desert-grassland ecological transition zone

Soil microorganisms are crucial to indicate ecosystem functions of terrestrial ecosystems. However, the responses of microbial communities to soil nutrient limitation in desert-grassland are still poorly understood. Hence, we investigated soil microbial community structures and metabolic characteristics in a desert-grassland ecological transition zone from the northern Loess Plateau, China, and explored the association of microbial communities with nutrient limitation via high-throughput sequencing. Threshold elemental ratios (TER) indicated that the microbial communities were strongly limited by nitrogen (N) under A. ordosica and P. tabuliformis communities. The phosphorus (P) limitation of microbial communities was observed in the aeolian sandy soil. The results imply that soil microbial communities had strong nutrient competition for N and P with aboveground vegetation in arid and oligotrophic ecosystems. The LEfSe and linear regression analysis revealed that the microbial taxa of Micrococcales, Micrococcaceae and Herpotrichiellaceae were significantly correlated with microbial N limitation. The Thermoleophilia taxa were significantly correlated with microbial P limitation. These biomarkers related to microbial nutrient limitation could be considered as the key microbial taxa to shape microbial communities and functions. Furthermore, N form had different effects on microbial communities, which NH₄⁺-N strongly affected bacterial communities, whereas NO₃^--N had a significant influence on fungal communities. The different responses indicate that soil microorganisms had corresponding nutrient preferences for bacterial and fungal communities, which might alleviate the nutrient limitations and environmental stress. This study provided important insights on microbial community structures linking to community functions and on the mechanisms governing microbial N and P limitation in arid land ecosystems.

Fluorescein Diacetate Hydrolysis Using the Whole Biofilm as a Sensitive Tool to Evaluate the Physiological State of Immobilized Bacterial Cells

Due to the increasing interest and the use of immobilized biocatalysts in bioremediation studies, there is a need for the development of an assay for quick and reliable measurements of their overall enzymatic activity. Fluorescein diacetate (FDA) hydrolysis is a widely used assay for measuring total enzymatic activity (TEA) in various environmental samples or in monoculture researches. However, standard FDA assays for TEA measurements in immobilized samples include performing an assay on cells detached from the carrier. This causes an error, because it is not possible to release all cells from the carrier without affecting their metabolic activity. In this study, we developed and optimized a procedure for TEA quantification in the whole biofilm formed on the carrier without disturbing it. The optimized method involves pre-incubation of immobilized carrier in phosphate buffer (pH 7.6) on the orbital shaker for 15 min, slow injection of FDA directly into the middle of the immobilized carrier, and incubation on the orbital shaker (130 rpm, 30 °C) for 1 h. Biofilm dry mass was obtained by comparing the dried weight of the immobilized carrier with that of the unimmobilized carrier. The improved protocol provides a simple, quick, and more reliable quantification of TEA during the development of immobilized biocatalysts compared to the original method.

Environmental and hydroclimatic factors influencing Vibrio populations in the estuarine zone of the Bengal delta

The objective of this study was to determine environmental parameters driving Vibrio populations in the estuarine zone of the Bengal delta. Spatio-temporal data were collected at river estuary, mangrove, beach, pond, and canal sites. Effects of salinity, tidal amplitude, and a cyclone and tsunami were included in the study. Vibrio population shifts were found to be correlated with tide-driven salinity and suspended particulate matter (SPM). Increased abundance of Vibrio spp. in surface water was observed after a cyclone, attributed to re-suspension of benthic particulate organic carbon (POC), and increased availability of chitin and dissolved organic carbon (DOC). Approximately a two log₁₀ increase in the (p < 0.05) number of Vibrio spp. was observed in < 20 μm particulates, compared with microphytoplankton (20-60 μm) and zooplankton > 60 μm fractions. Benthic and suspended sediment comprised a major reservoir of Vibrio spp. Results of microcosm experiments showed enhanced growth of vibrios was related to concentration of organic matter in SPM. It is concluded that SPM, POC, chitin, and salinity significantly influence abundance and distribution of vibrios in the Bengal delta estuarine zone.

Near Real-Time Detection of E. coli in Reclaimed Water

Advanced treatment of reclaimed water prior to potable reuse normally results in the inactivation of bacterial populations, however, incremental treatment failure can result in bacteria, including pathogens, remaining viable. Therefore, potential microorganisms need to be detected in real-time to preclude potential adverse human health effects. Real-time detection of microbes presents unique problems which are dependent on the water quality of the test water, including parameters such as particulate content and turbidity, and natural organic matter content. In addition, microbes are unusual in that: (i) viability and culturability are not always synonymous; (ii) viability in water can be reduced by osmotic stress; and (iii) bacteria can invoke repair mechanisms in response to UV disinfection resulting in regrowth of bacterial populations. All these issues related to bacteria affect the efficacy of real-time detection for bacteria. Here we evaluate three different sensors suitable for specific water qualities. The sensor A is an on-line, real-time sensor that allows for the continuous monitoring of particulates (including microbial contaminants) using multi-angle-light scattering (MALS) technology. The sensor B is a microbial detection system that uses optical technique, Mie light scattering, for particle sizing and fluorescence emission for viable bacteria detection. The last sensor C was based on adenosine triphosphate (ATP) production. E. coli was used a model organism and out of all tested sensors, we found the sensor C to be the most accurate. It has a great potential as a surrogate parameter for microbial loads in test waters and be useful for process control in treatment trains.

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor

Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34–59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2′-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.

Different Metabolomic Responses to Carbon Starvation between Light and Dark Conditions in the Purple Photosynthetic Bacterium, Rhodopseudomonas palustris

Purple photosynthetic bacteria utilize light energy for growth. We previously demonstrated that light energy contributed to prolonging the survival of multiple purple bacteria under carbon-starved conditions. In order to clarify the effects of illumination on metabolic states under carbon-starved, non-growing conditions, we herein compared the metabolic profiles of starved cells in the light and dark using the purple bacterium, Rhodopseudomonas palustris. The metabolic profiles of starved cells in the light were markedly different from those in the dark. After starvation for 5 d in the light, cells showed increases in the amount of ATP and the NAD⁺/NADH ratio. Decreases in the amounts of most metabolites related to glycolysis and the TCA cycle in energy-rich starved cells suggest the active utilization of these metabolites for the modification of cellular components. Starvation in the dark induced the consumption of cellular compounds such as amino acids, indicating that the degradation of these cellular components produced ATP in order to maintain viability under energy-poor conditions. The present results suggest that intracellular energy levels alter survival strategies under carbon-starved conditions through metabolism.

Differential Effect of Food Sanitizers on Formation of Viable but Nonculturable Salmonella enterica in Poultry

A method for microscopic enumeration of viable Salmonella enterica in meat samples was developed by using the LIVE/DEAD BacLight kit technology. A two-step centrifugation and wash process was developed to clean the samples from food and chemical impurities that might otherwise interfere with the appropriate staining reactions. The accuracy of the BacLight kit-based viability assessments was confirmed with various validation tests that were conducted by following the manufacturer's instructions. For the biocide challenge tests, chicken parts each bearing around 8.5 log of S. enterica were sprayed with common food sanitizers such as 1,3-dibromo-5,5-dimethylhydantoin (DBDMH), lactic acid (LA), and peracetic acid (PAA). The log reduction (LR) of S. enterica for each test biocide was evaluated by microscopic and conventional culture plate methods. The results show that both LA and PAA treatments generated a greater number of microscopic counts compared with the corresponding plate counts with differences being around half a log. This discrepancy is believed to occur when cells enter a so-called viable but nonculturable (VBNC) state, and to our knowledge, this is the first report documenting the presence of VBNC in PAA- and LA-treated food samples. In contrast, the BacLight-based viable counts were comparable to the culture-based enumerations of all DBDMH-treated samples. Therefore, we concluded that DBDMH-treated meat did not contain significant VBNC populations of S. enterica. A detailed description of our spray system, the dye validation, and the treatment reproducibility are also provided in this work.