Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems

Earth's most needed uncultivated aquatic prokaryotes

Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.

Microbial community structure and water quality performance in local scrubber reclaim system for water reclamation of the semiconductor industry: A case study of a semiconductor plant in Beijing

The local scrubber reclaim (LSR) system plays a critical role in water reclamation and in reducing environmental pollution emissions in semiconductor factories. This study monitored the changes in water quality and assessed the key stages of pollutant removal, with a primary focus on evaluating microbial growth and the shifts in microbial community structure and function in the LSR system. The results showed that activated carbon filtration (ACF) effectively removed total organic carbon (TOC) with a removal rate of 59.35%, while ion exchange (IEX) was essential for reducing conductivity, with a removal rate of 87.33%. Furthermore, severe bacterial growth was observed (more than 1000 CFU/ml) in the system. Bacteria numbers in the MMF and ACF stages grew dramatically, at least four times higher than that in the influent tank. After chlorination in the storage tank, microbial numbers sharply dropped, yet microbial diversity increased. The dominant microbial group in the LSR system was Patescibacteria (average relative abundance was 32.37%), considered part of the "microbial dark matter" and also known as Candidate Phyla Radiation (CPR). Following the effluent from the storage tank, the biofilm-forming potential of bacteria significantly increased (relative abundance rose from 7.19% to 15.20%), along with a varying increase in the abundance of genes related to metabolism. Measures should be implemented to prevent pipeline blockage and improve water reclamation efficiency.

Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community

Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.

Assessing microbial growth in drinking water using nucleic acid content and flow cytometry fingerprinting

This study utilizes flow cytometry (FCM) to evaluate the high nucleic acid (HNA) and low nucleic acid (LNA) content of intact cells for monitoring bacterial dynamics in drinking water treatment and supply systems. Our findings indicate that chlorine and nutrients differently impact components of bacterial populations. HNA bacteria, characterized by high metabolic rates, quickly react to nutrient alterations, making them suitable indicators of growth under varying water treatment and supply conditions. Conversely, LNA bacteria adapt to environments with stable, slowly degradable organics, reflecting distinct physiological characteristics. Changes in water treatment and supply conditions, such as chlorine dosing and nutrient inputs, significantly impact the ratio between HNA and LNA. FCM fingerprinting combined with cluster analysis provides a more sensitive evaluation of water quality by capturing a broader range of microbial characteristics compared to using only HNA/LNA ratios. This work advocates for multi-parameter data analysis to advance monitoring techniques for water treatment and supply processes.

Beyond genomics in Patescibacteria: A trove of unexplored biology packed into ultrasmall bacteria

Patescibacteria, also known as the Candidate Phyla Radiation, are a diverse clade of largely uncultivated, small bacteria that comprise a significant proportion of all bacterial diversity. The few members that have been cultivated exhibit a fascinating life cycle in which they grow as obligate epibionts on the surface of host bacteria. In this Perspective, we make the case that the study of these unique, divergent, and poorly characterized organisms represents an exciting frontier in microbiology. This burgeoning field has already achieved several critical breakthroughs, including metagenomic sequence-based reconstructions of the metabolic and biosynthetic capabilities of diverse Patescibacteria and the development of generalizable strategies for their cultivation and genetic manipulation. We argue these that advances, among others, should pave the way toward a molecular understanding of the complex interactions that undoubtedly underpin the relationship between Patescibacteria and their hosts.

Riverine bacterial communities are more shaped by species sorting in intensive urban and agricultural watersheds

Bacterial communities play a crucial role in maintaining the stability of river ecosystems and driving biogeochemical cycling, exhibiting high sensitivity to environmental change. However, understanding the spatial scale effects and assembly mechanisms of riverine bacterial communities under distinct anthropogenic disturbances remains a challenge. Here, we investigated bacterial communities across three distinct watersheds [i.e., intensive urban (UW), intensive agricultural (AW), and natural (NW)] in both dry and wet seasons. We explored biogeographic patterns of bacterial communities and the influence of landscape patterns at multi-spatial scales and water chemistry on bacterial communities. Results showed that α diversity was significantly lower in UW and AW compared to NW, particularly in the dry season. A gradient of β diversity with NW > UW > AW was observed across both seasons (p < 0.05). Pseudomonadota, Bacteroidota, and Actinobacteriota were the most abundant phyla across all watersheds, with specific taxa enriched in each watershed (i.e., the class Actinobacteria was significant enrichment in UW and AW, and Clostridia in NW). The influence of landscape patterns on bacterial communities was significantly lower in human-disturbed watersheds, particularly in UW, where this influence also varied slightly from near riparian buffers to sub-watershed. Homogeneous selection and drift jointly dominated the bacterial community assembly across all watersheds, with homogeneous selection exhibiting a greater influence in UW and AW. Landscape patterns explained less variance in bacterial communities in UW and AW than in NW, and more variance was explained by water chemistry (particularly in UW). These suggest that the stronger influence of species sorting in UW and AW was driven by more allochthonous inputs of water chemistry (greater environmental stress). These findings provide a theoretical foundation for a deeper understanding of riverine bacterial community structure, spatial scale effects, and ecological management under different anthropogenic activities.

Microplastics alter the functioning of marine microbial ecosystems

Microplastics pervade ocean ecosystems. Despite their effects on individuals or populations are well documented, the consequences of microplastics on ecosystem functioning are still largely unknown. Here, we show how microplastics alter the structure and functioning of pelagic microbial ecosystems. Using experimental pelagic mesocosms, we found that microplastics indirectly affect marine productivity by changing the bacterial and phytoplankton assemblages. Specifically, the addition of microplastics increased phytoplankton biomass and shifted bacterial assemblages' composition. Such changes altered the interactions between heterotrophic and autotrophic microbes and the cycling of ammonia in the water column, which ultimately benefited photosynthetic efficiency. The effects of microplastics on marine productivity were consistent for different microplastic types. This study demonstrates that microplastics affect bacteria and phytoplankton communities and influence marine productivity, which ultimately alters the functioning of the whole ocean ecosystem.

Rethinking characterization, application, and importance of extracellular polymeric substances in water technologies

Biofilms play important roles in water technologies such as membrane treatments and activated sludge. The extracellular polymeric substances (EPS) are key components of biofilms. However, the precise nature of these substances and how they influence biofilm formation and behavior remain critical knowledge gaps. EPS are produced by many different microorganisms and span multiple biopolymer classes, which each require distinct strategies for characterization. The biopolymers additionally associate with each other to form insoluble complexes. Here, we explore recent progress toward resolving the structures and functions of EPS, where a shift towards direct functional assessments and advanced characterization techniques is necessary. This will enable integration with better microbial community and omics analyses to understand EPS biosynthesis pathways and create further opportunities for EPS control and valorization.

Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period

Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.

Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria

Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.

The size and diversity of microbes determine carbon use efficiency in soil

Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.

Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation

The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.

Anthropogenic original DOM is a critical factor affecting LNA bacterial community assembly

We investigated the geographical and environmental distance-decay relationships for both of the two bacteria in the Haihe River, Tianjin, China. HNA bacteria exhibited a stronger geographical variation-dependent pattern while LNA bacteria exhibited a stronger environmental variation-dependent pattern. Variance partition analysis (VPA), Mantel test, and partial mantel test validated the discrepant impacts of geographical distance and environmental factors on their two communities. The heterogeneous selection dominated community assembly of LNA bacteria demonstrates their greater sensitivity to environmental conditions. As the deterministic environmental factor, anthropogenic original dissolved organic matter (DOM) functions exclusively on LNA bacteria, and it is the critical factor leading to the discrepant biogeographical patterns of LNA and HNA bacteria. LNA bacteria interact with HNA bacteria and mediate the DOM driving total bacteria assembly. The LNA keystone taxa, Pseudomonas, Rheinheimera, Candidatus Aquiluna, and hgcl clade are capable to compete with HNA bacteria for anthropogenic original DOM, and are potential indicators of anthropogenic pollution. Our research reveals the non-negligible effect of the LNA bacteria in regulating the ecological response of total bacteria.

Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes

Planktonic bacteria can be grouped into 'high nucleic acid content (HNA) bacteria' and 'low nucleic acid content (LNA) bacteria.' Nutrient input modes vary in environments, causing nutrient availability heterogeneity. We incubated them with equal amounts of total glucose added in a continuous/pulsed mode. The pulse-treated LNA bacteria exhibited twice the cell abundance and four times the viability of the continuous-treated LNA, while HNA did not show an adaptation to pulsed treatment. In structural equation modelling, LNA bacteria had higher path coefficients than HNA, between growth and carbon-saving metabolic pathways, intracellular ATP and the inorganic energy storage polymer, polyphosphate, indicating their low-cost growth, and flexible energy storage and utilisation. After incubation, the pulse-treated LNA bacteria contained more proteins and polysaccharides (0.00064, 0.0012 ng cell-1 ) than the continuous-treated LNA (0.00014, 0.00014 ng cell-1 ), conferring endurance and rapid response to pulses. Compared to LNA, HNA keystone taxa had stronger correlations with the primary glucose metabolism step, glycolysis, and occupied leading positions to explain the random forest model. They are essential to introduce glucose into the element cycling of the whole community under both treatments. Our work outlines a systematic bacterial response to carbon input.

Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival

Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.

Spatiotemporal dynamics of high and low nucleic acid-content bacterial communities in Chinese coastal seawater: assembly process, co-occurrence relationship and the ecological functions

Studies of high nucleic acid-content (HNA) and low nucleic acid-content (LNA) bacterial communities are updating our view of their distributions and taxonomic composition. However, there are still large gaps in our knowledge of the composition, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities. Here, using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics, assembly processes, co-occurrence relationships and ecological functions of HNA and LNA bacterial communities in the samples collected in summer and winter in Chinese coastal seas. The communities of HNA and LNA bacteria had clear spatiotemporal patterns and LNA bacteria was phylogenetically less diverse than HNA bacteria in both seasons. The distribution of HNA and LNA bacteria were significantly affected by the environmental factors and a significant seasonal-consistent distance-decay patterns were found in HNA and LNA bacteria. Furthermore, a quantitative assessment of ecological processes revealed that dispersal limitation, homogeneous selection exerted important roles in the community assembly of HNA and LNA bacteria. More importantly, we observed seasonality in the co-occurrence relationships: closer inter-taxa connections of HNA bacterial communities in winter than in summer and the opposite is true in the LNA bacterial communities. Some ecological functions, such as: phototrophy, photoautotrophy, oxygenic photoautotrophy, were different between HNA and LNA bacteria. These results provide a better understanding of spatiotemporal patterns, processes, and the ecological functions of HNA and LNA bacterial communities in Chinese coastal seawater.

Presence of an ultra-small microbiome in fermented cabbages

Background

Ultramicrobacteria (UMB), also known as ultra-small bacteria, are tiny bacteria with a size less than 0.1 µm³. They have a high surface-to-volume ratio and are found in various ecosystems, including the human body. UMB can be classified into two types: one formed through cell contraction and the other that maintains a small size. The ultra-small microbiome (USM), which may contain UMB, includes all bacteria less than 0.2 µm in size and is difficult to detect with current methods. However, it poses a potential threat to food hygiene, as it can pass through sterilization filters and exist in a viable but non-culturable (VBNC) state. The data on the USM of foods is limited. Some bacteria, including pathogenic species, are capable of forming UMB under harsh conditions, making it difficult to detect them through conventional culture techniques.

Methods

The study described above focused on exploring the diversity of USM in fermented cabbage samples from three different countries (South Korea, China, and Germany). The samples of fermented cabbage (kimchi, suancai, and sauerkraut) were purchased and stored in chilled conditions at approximately 4 °C until filtration. The filtration process involved two steps of tangential flow filtration (TFF) using TFF cartridges with different pore sizes (0.2 µm and 100 kDa) to separate normal size bacteria (NM) and USM. The USM and NM isolated via TFF were stored in a refrigerator at 4 °C until DNA extraction. The extracted DNA was then amplified using PCR and the full-length 16S rRNA gene was sequenced using single-molecule-real-time (SMRT) sequencing. The transmission electron microscope (TEM) was used to confirm the presence of microorganisms in the USM of fermented cabbage samples.

Results

To the best of our knowledge, this is the first study to identify the differences between USM and NM in fermented cabbages. Although the size of the USM (average 2,171,621 bp) was smaller than that of the NM (average 15,727,282 bp), diversity in USM (average H' = 1.32) was not lower than that in NM (average H' = 1.22). In addition, some members in USM probably underwent cell shrinkage due to unfavorable environments, while others maintained their size. Major pathogens were not detected in the USM in fermented cabbages. Nevertheless, several potentially suspicious strains (genera Cellulomonas and Ralstonia) were detected. Our method can be used to screen food materials for the presence of USM undetectable via conventional methods. USM and NM were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The USM of fermented vegetables exhibited differences in size, diversity, and composition compared with the conventional microbiome. This study could provide new insights into the ultra-small ecosystem in fermented foods, including fermented cabbages.

Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics

Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.

Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system

BACKGROUND

Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system.

RESULTS

We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes.

CONCLUSIONS

These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.

Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota

Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.

Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.

A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland

The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.

Revisiting Mt Fuji's groundwater origins with helium, vanadium and environmental DNA tracers

Known locally as the water mountain, for millennia Japan's iconic Mt Fuji has provided safe drinking water to millions of people via a vast network of groundwater and freshwater springs. Groundwater, which is recharged at high elevations, flows down Fuji's flanks within three basaltic aquifers, ultimately forming countless pristine freshwater springs among Fuji's foothills. Here we challenge the current conceptual model of Fuji being a simple system of laminar groundwater flow with little to no vertical exchange between its three aquifers. This model contrasts strongly with Fuji's extreme tectonic instability due to its unique location on top of the only known continental trench-trench-trench triple junction, its complex geology and its unusual microbial spring water communities. On the basis of a unique combination of microbial environmental DNA, vanadium and helium tracers, we provide evidence for prevailing deep circulation and a previously unknown deep groundwater contribution to Fuji's freshwater springs. The most substantial deep groundwater upwelling has been found along Japan's most tectonically active region, the Fujikawa-kako Fault Zone. Our findings broaden the hydrogeological understanding of Fuji and demonstrate the vast potential of combining environmental DNA, on-site noble gas and trace element analyses for groundwater science.

Microbial Water Quality through a Full-Scale Advanced Wastewater Treatment Demonstration Facility

The fates of viruses, bacteria, and antibiotic resistance genes during advanced wastewater treatment are important to assess for implementation of potable reuse systems. Here, a full-scale advanced wastewater treatment demonstration facility (ozone, biological activated carbon filtration, micro/ultrafiltration, reverse osmosis, and advanced oxidation) was sampled over three months. Atypically, no disinfectant residual was applied before the microfiltration step. Microbial cell concentrations and viability were assessed via flow cytometry and adenosine triphosphate (ATP). Concentrations of bacteria (16S rRNA gene), viruses (human adenovirus and JC polyomavirus), and antibiotic resistance genes (sul1 and bla _TEM ) were assessed via quantitative PCR following the concentration of large sample volumes by dead-end ultrafiltration. In all membrane filtration permeates, microbial concentrations were higher than previously reported for chloraminated membranes, and log₁₀ reduction values were lower than expected. Concentrations of 16S rRNA and sul1 genes were reduced by treatment but remained quantifiable in reverse osmosis permeate. It is unclear whether sul1 in the RO permeate was from the passage of resistance genes or new growth of microorganisms, but the concentrations were on the low end of those reported for conventional drinking water distribution systems. Adenovirus, JC polyomavirus, and bla _TEM genes were reduced below the limit of detection (∼10^-2 gene copies per mL) by microfiltration. The results provide insights into how treatment train design and operation choices affect microbial water quality as well as the use of flow cytometry and ATP for online monitoring and process control.

Microbial marker for seawater intrusion in a coastal Mediterranean shallow Lake, Lake Vrana, Croatia

Climate change-induced rising sea levels and prolonged dry periods impose a global threat to the freshwater scarcity on the coastline: salinization. Lake Vrana is the largest surface freshwater resource in mid-Dalmatia, while the local springs are heavily used in agriculture. The karstified carbonate ridge that separates this shallow lake from the Adriatic Sea enables seawater intrusion if the lakes' precipitation-evaporation balance is disturbed. In this study, the impact of anthropogenic activities and drought exuberated salinization on microbial communities was tracked in Lake Vrana and its inlets, using 16S rRNA gene sequencing. The lack of precipitation and high water temperatures in summer months introduced an imbalance in the water regime of the lake, allowing for seawater intrusion, mainly via the karst conduit Jugovir. The determined microbial community spatial differences in the lake itself and the main drainage canals were driven by salinity, drought, and nutrient loading. Particle-associated and free-living microorganisms both strongly responded to the ecosystem perturbations, and their co-occurrence was driven by the salinization event. Notably, a bloom of halotolerant taxa, predominant the sulfur-oxidizing genus Sulfurovum, emerged with increased salinity and sulfate concentrations, having the potential to be used as an indicator for salinization of shallow coastal lakes. Following summer salinization, lake water column homogenization took from a couple of weeks up to a few months, while the entire system displayed increased salinity despite increased precipitation. This study represents a valuable contribution to understanding the impact of the Freshwater Salinization Syndrome on Mediterranean lakes' microbial communities and the ecosystem resilience.

Characterization of chlorinated paraffin-degrading bacteria from marine estuarine sediments

This study explored chlorinated paraffin (CP)-degrading bacteria from the marine environment. Aequorivita, Denitromonas, Parvibaculum, Pseudomonas and Ignavibacterium were selected as the dominant genera after enrichment with chlorinated paraffin 52 (CP52) as the sole carbon source. Eight strains were identified as CP degraders, including Pseudomonas sp. NG6 and NF2, Erythrobacter sp. NG3, Castellaniella sp. NF6, Kordiimonas sp. NE3, Zunongwangia sp. NF12, Zunongwangia sp. NH1 and Chryseoglobus sp. NF13, and their degradation efficiencies ranged from 6.4% to 19.0%. In addition to Pseudomonas, the other six genera of bacteria were first reported to have the degradation ability of CPs. Bacterial categories, carbon-chain lengths and chlorination degrees were three crucial factors affecting the degradation efficiencies of CPs, with their influential ability of chlorinated degrees > bacterial categories > carbon-chain lengths. CP degradation can be performed by producing chlorinated alcohols, chlorinated olefins, dechlorinated alcohols and lower chlorinated CPs. This study will provide valuable information on CP biotransformation and targeted bacterial resources for studying the transformation processes of specific CPs in marine environments.

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to “protein metabolism,” and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the “cell wall and capsule” of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM.

Investigation of the effect of sustainable magnetic treatment on the microbiological communities in drinking water

The drinking water scarcity is posing a threat to mankind, hence better water quality management methods are required. Magnetic water treatment, which has been reported to improve aesthetic water quality and reduce scaling problems, can be an important addition to the traditional disinfectant dependent treatment. Despite the extensive market application opportunities, the effect of magnetic fields on (microbial) drinking water communities and subsequently the biostability is still largely unexplored, although the first patent was registered already 1945. Here flow cytometry was applied to assess the effect of weak magnetic fields (≤10 G) with strong gradients (≈800 G/m) on drinking water microbial communities. Drinking water was collected from the tap and placed inside the magnetic field (treated) and 5 m away from the magnet to avoid any background interferences (control) using both a static set-up and a shaking set-up. Samples were collected during a seven-day period for flow cytometry examination. Additionally, the effects of magnetic fields on the growth of Pseudomonas aeruginosa in autoclaved tap water were examined. Based on the fluorescent intensity of the stained nucleic acid content, the microbial cells were grouped into low nucleic acid content (LNA) and high nucleic acid content (HNA). Our results show that the LNA was dominant under nutrient limited condition while the HNA dominates when nutrient is more available. Such behavior of LNA and HNA matches well with the long discussed r/K selection model where r-strategists adapted to eutrophic conditions and K-strategists adapted to oligotrophic conditions. The applied magnetic fields selectively promote the growth of LNA under nutrient rich environment, which indicates a beneficial effect on biostability enhancement. Inhibition on an HNA representative Pseudomonas aeruginosa has also been observed. Based on our laboratory observations, we conclude that magnetic field treatment can be a sustainable method for microbial community management with great potential.

Holistic approach to chemical and microbiological quality of aquatic ecosystems impacted by wastewater effluent discharges

Wastewater treatment plants (WWTPs) collect wastewater from various sources and use different treatment processes to reduce the load of pollutants in the environment. Since the removal of many chemical pollutants and bacteria by WWTPs is incomplete, they constitute a potential source of contaminants. The continuous release of contaminants through WWTP effluents can compromise the health of the aquatic ecosystems, even if they occur at very low concentrations. The main objective of this work was to characterize, over a period of four months, the treatment steps starting from income to the effluent and 5 km downstream to the receiving river. In this context, the efficiency removal of chemical pollutants (e.g. hormones and pharmaceuticals, including antibiotics) and bacteria was assessed in a WWTP case study by using a holistic approach. It embraces different chemical and biological-based methods, such as pharmaceutical analysis by HPLC-MSMS, growth rate inhibition in algae, ligand binding estrogen receptor assay, microbial community study by 16S and shotgun sequencing along with relative quantification of resistance genes by quantitative polymerase chain reaction. Although both, chemical and biological-based methods showed a significant reduction of the pollutant burden in effluent and surface waters compared to the influent of the WWTP, no complete removal of pollutants, pathogens and antibiotic resistance genes was observed.

A systematic review on chlorine tolerance among bacteria and standardization of their assessment protocol in wastewater

Though chlorine is a cost-effective disinfectant for water and wastewaters, the bacteria surviving after chlorination pose serious public health and environmental problems. This review critically assesses the mechanism of chlorine disinfection as described by various researchers; factors affecting chlorination efficacy; and the re-growth potential of microbial contaminations in treated wastewater post chlorination to arrive at meaningful doses for ensuring health safety. Literature analysis shows procedural inconsistencies in the assessment of chlorine tolerant bacteria, making it extremely difficult to compare the tolerance characteristics of different reported tolerant bacteria. A comparison of logarithmic reduction after chlorination and the concentration-time values for prominent pathogens led to the generation of a standard protocol for the assessment of chlorine tolerance. The factors that need to be critically monitored include applied chlorine doses, contact time, determination of chlorine demands of the medium, and the consideration of bacterial counts immediately after chlorination and in post chlorinated samples (regrowth). The protocol devised here appropriately assesses the chlorine-tolerant bacteria and urges the scientific community to report the regrowth characteristics as well. This would increase the confidence in data interpretation that can provide a better understanding of chlorine tolerance in bacteria and aid in formulating strategies for effective chlorination.

Characteristics, Biodiversity, and Cultivation Strategy of Low Nucleic Acid Content Bacteria

Low nucleic acid content (LNA) bacteria are ubiquitous and estimated to constitute 20%–90% of the total bacterial community in marine and freshwater environment. LNA bacteria with unique physiological characteristics, including small cell size and small genomes, can pass through 0.45-μm filtration. The researchers came up with different terminologies for low nucleic acid content bacteria based on different research backgrounds, such as: filterable bacteria, oligotrophic bacteria, and low-DNA bacteria. LNA bacteria have an extremely high level of genetic diversity and play an important role in material circulation in oligotrophic environment. However, the majority of LNA bacteria in the environment remain uncultivated. Thus, an important challenge now is to isolate more LNA bacteria from oligotrophic environments and gain insights into their unique metabolic mechanisms and ecological functions. Here, we reviewed LNA bacteria in aquatic environments, focusing on their characteristics, community structure and diversity, functions, and cultivation strategies. Exciting future prospects for LNA bacteria are also discussed.

Characteristics and origin of clogging-functional bacteria during managed aquifer recharge: A laboratory study

Owing to serious influences on well performance, bacteria-induced clogging has become a dilemma for managed aquifer recharge (MAR). During MAR, surface river water is inoculated into aquifer and mixed with groundwater. Therefore, the clogging-functional bacteria may originate from the river water or the groundwater. However, the origin of the clogging-functional bacteria in the aquifer has not yet been well understood. This study conducted a series of laboratory-scale column experiments involving different recharge modes (using river water, groundwater) to simulate the processes of bacteria-induced clogging and used the high-throughput sequencing technology, aiming to elucidate the community characteristics and the origin of the clogging-functional bacteria involved in MAR bioclogging. Analyses of the bacterial-community characteristics showed significant differences between the river water and groundwater. The bacterial-community characteristics of the clogging aquifer in the different recharge modes were similar to each other and have common genera, namely, Acinetobacter, Brevundimonas, Exiguobacterium, Porphyrobacter, Cloacibacterium, and Sphingobium, which suggests that MAR activity could promote bacterial communities to become identical during surface water infiltration into aquifers, despite differences in the bacterial communities present in the subsurface- and surface systems. This knowledge will assist greatly in targeted treatment and prophylaxis of clogging-functional bacteria during managed aquifer recharge.

Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome

Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of ¹³C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a ¹³C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a ¹³C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.

IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.

Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding

AIMS

The aim was to characterize indigenous microorganisms in oil reservoirs after polymer flooding (RAPF).

METHODS

The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1~0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing.

RESULTS

Indigenous microorganisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences of bacterial compositions were observed among the three phases of the same well and among the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well.

CONCLUSIONS

The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional microorganisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous microorganisms for MEOR.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.

Variation of High and Low Nucleic Acid-Content Bacteria in Tibetan Ice Cores and Their Relationship to Black Carbon

Nutrient enrichment caused by black carbon (BC) is a major ecological crisis in glacial ecosystems. The microbiological effects of BC were assessed in this study by using fluorescent fingerprinting assay based on flow cytometry (FCM) of bacterial communities with low (LNA) and high (HNA) nucleic acid-content bacteria. Here, we investigated a high-resolution temporal variation of bacterial abundance and LNA/HNA ratio in Tibetan ice cores. Our results revealed that bacterial abundance was proportional to the atmospheric BC on the glaciers. The shift of LNA functional groups to HNA functional groups in glaciers suggested BC emissions increased the proportion of highly active cells. In addition, distinct number of LNA and HNA functional groups was identified between the monsoon and non-monsoon seasons. Westerly winds with high amounts of BC accounted for high ratio of HNA functional groups during the non-monsoon season. In comparison, high moisture during the monsoon season decreased atmospheric BC loading, which increases the ratio of LNA functional groups. Correlations between BC and functional groups were very strong, showing that two functional groups may serve as early-warning indicators of microbiological effects of BC at low trophic level. Our approach provides a potential early-warning framework to study the influences of atmospheric BC on the glaciological community.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

Pathogenic and Indigenous Denitrifying Bacteria are Transcriptionally Active and Key Multi-Antibiotic-Resistant Players in Wastewater Treatment Plants

The global rise and spread of antibiotic resistance greatly challenge the treatment of bacterial infections. Wastewater treatment plants (WWTPs) harbor and discharge antibiotic resistance genes (ARGs) as environmental contaminants. However, the knowledge gap on the host identity, activity, and functionality of ARGs limits transmission and health risk assessment of the WWTP resistome. Hereby, a genome-centric quantitative metatranscriptomic approach was exploited to realize high-resolution qualitative and quantitative analyses of bacterial hosts of ARGs (i.e., multiresistance, pathogenicity, activity, and niches) in the 12 urban WWTPs. We found that ∼45% of 248 recovered genomes expressed ARGs against multiple classes of antibiotics, among which bacitracin and aminoglycoside resistance genes in Proteobacteria were the most prevalent scenario. Both potential pathogens and indigenous denitrifying bacteria were transcriptionally active hosts of ARGs. The almost unchanged relative expression levels of ARGs in the most resistant populations (66.9%) and the surviving ARG hosts including globally emerging pathogens (e.g., Aliarcobacter cryaerophilus) in treated WWTP effluent prioritize future examination on the health risks related to resistance propagation and human exposure in the receiving environment.

Bacterial dynamics in drinking water distribution systems and flow cytometry monitoring scheme optimization

Water biostability is desired within drinking water distribution systems (DWDSs) to limit microbiologically-related operational, aesthetic and, eventually, health-related issues. However, variations in microbiological quality can take place both spatially along DWDS pipelines and temporally at single locations due to biofilm detachment, water quality seasonality and other processes. In this study, long- and short-term trends of bacterial concentration and community structure were investigated in a secondary branch of an unchlorinated DWDS for several months using high-frequency flow cytometry (FCM) and traditional laboratory monitoring campaigns. Long-term trends of bacterial concentrations and community structures were likely caused by changes in the water physical-chemical quality (i.e. pH and conductivity). Short-term daily pattern, instead, resulted in significant variations between the bacterial concentrations and community structures at different hours, likely due to biofilm detachment and loose deposits resuspension related to changes in the local water flow. These patterns, however, showed broad variations and did not persist during the entire monitoring campaign presumably due to the stochasticity of local instantaneous demand and seasonal changes in water consumption. During periods without sensible long-term trends, the sampling hours explain a comparable or larger fraction of the bacterial community diversity compared to dates. The variations observed with FCM were poorly or not detected by traditional laboratory analyses, as the correlation between the two were rather weak, highlighting the limited information provided by traditional approaches. On the other hand, FCM data correlated with water pH and conductivity, underlining the relation between physical-chemical and microbiological water quality. Such results suggest that the advanced control of the physical-chemical water quality could minimize the microbiological water quality variations. Moreover, monitoring campaign planning should take into account the sampling time to reduce the noise caused by daily fluctuations and/or assess the overall quality variations. Finally, as monitoring costs are one of the barriers which prevent a more widespread use of FCM, a monitoring scheme optimization strategy was developed. Such strategy employs the data from an initial high-frequency sampling period to select the sampling hours which maximize the observed variations of bacterial concentration and community composition.

Automated Online Flow Cytometry Advances Microalgal Ecosystem Management as in situ, High-Temporal Resolution Monitoring Tool

Microalgae are emerging as a next-generation biotechnological production system in the pharmaceutical, biofuel, and food domain. The economization of microalgal biorefineries remains a main target, where culture contamination and prokaryotic upsurge are main bottlenecks to impair culture stability, reproducibility, and consequently productivity. Automated online flow cytometry (FCM) is gaining momentum as bioprocess optimization tool, as it allows for spatial and temporal landscaping, real-time investigations of rapid microbial processes, and the assessment of intrinsic cell features. So far, automated online FCM has not been applied to microalgal ecosystems but poses a powerful technology for improving the feasibility of microalgal feedstock production through in situ, real-time, high-temporal resolution monitoring. The study lays the foundations for an application of automated online FCM implying far-reaching applications to impel and facilitate the implementation of innovations targeting at microalgal bioprocesses optimization. It shows that emissions collected on the FL1/FL3 fluorescent channels, harnessing nucleic acid staining and chlorophyll autofluorescence, enable a simultaneous assessment (quantitative and diversity-related) of prokaryotes and industrially relevant phototrophic Chlorella vulgaris in mixed ecosystems of different complexity over a broad concentration range (2.2–1,002.4 cells ⋅μL^–1). Automated online FCM combined with data analysis relying on phenotypic fingerprinting poses a powerful tool for quantitative and diversity-related population dynamics monitoring. Quantitative data assessment showed that prokaryotic growth phases in engineered and natural ecosystems were characterized by different growth speeds and distinct peaks. Diversity-related population monitoring based on phenotypic fingerprinting indicated that prokaryotic upsurge in mixed cultures was governed by the dominance of single prokaryotic species. Automated online FCM is a powerful tool for microalgal bioprocess optimization owing to its adaptability to myriad phenotypic assays and its compatibility with various cultivation systems. This allows advancing bioprocesses associated with both microalgal biomass and compound production. Hence, automated online FCM poses a viable tool with applications across multiple domains within the biobased sector relying on single cell–based value chains.

Changes in biofilm composition and microbial water quality in drinking water distribution systems by temperature increase induced through thermal energy recovery

Drinking water distribution systems (DWDSs) have been thoroughly studied, but the concept of thermal energy recovery from DWDSs is very new and has been conceptualized in the past few years. Cold recovery results in a temperature increase of the drinking water. Its effects on drinking water quality and biofilm development are unclear. Hence, we studied both bulk water and biofilm phases for 232 days in two parallel pilot scale distribution systems with two temperature settings after cold recovery, 25 °C and 30 °C, and compared these with a reference pilot system without cold recovery. In all three pilot distributions systems (DSs) our results showed an initial increase in biomass (ATP) in the biofilm phase, along with occurrence of primary colonizers (Betaproteobacteriales) and subsequently a decrease in biomass and an increasing relative abundance of other microbial groups (amoeba resisting groups; Xanthobacteraceae, Legionellales), including those responsible for EPS formation in biofilms (Sphingomonadaceae). The timeline for biofilm microbial development was different for the three pilot DSs: the higher the temperature, the faster the development took place. With respect to the water phase within the three pilot DSs, major microbial contributions came from the feed water (17-100%) and unkown sources (2-80%). Random contributions of biofilm (0-70%) were seen between day 7-77. During this time period six-fold higher ATP concentration (7-11 ng/l) and two-fold higher numbers of high nucleic acid cells (5.20-5.80 × 10⁴ cells/ml) were also observed in the effluent water from all three pilot DSs, compared to the feed water. At the end of the experimental period the microbial composition of effluent water from three pilot DSs revealed no differences, except the presence of a biofilm related microbial group (Sphingomonadaceae), within all three DSs compared to the feed water. In the biofilm phase higher temperatures initiated the growth of primary colonizing bacteria but this did not lead to differences in microbial diversity and composition at the end of the experimental period. Hence, we propose that the microbiological water quality of DWDSs with cold recovery should be monitored more frequently during the first 2-3 months of operation.

Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome

Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in the utilization of amino acids, organic acids and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-day lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed that COGs associated with energy production increased in number in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within a short residence time of lotic freshwater systems.

The microbial dimension of submarine groundwater discharge: current challenges and future directions

Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.

Effects of oxygen exposure on relative nucleic acid content and membrane integrity in the human gut microbiota

While the diversity of the human gut microbiota is becoming increasingly well characterized, bacterial physiology is still a critical missing link in understanding how the gut microbiota may be implicated in disease. The current best practice for studying bacterial physiology involves the immediate storage of fecal samples in an anaerobic chamber. This reliance on immediate access to anaerobic chambers greatly limits the scope of sample populations that can be studied. Here, we assess the effects of short-term oxygen exposure on gut bacterial physiology and diversity. We use relative nucleic acid content and membrane integrity as markers of bacterial physiology, and 16S rRNA gene amplicon sequencing to measure bacterial diversity. Samples were stored for up to 6 h in either ambient conditions or in anoxic environments created with gas packs or in an anaerobic chamber. Our data indicate that AnaeroGen sachets preserve bacterial membrane integrity and nucleic acid content over the course of 6 h similar to storage in an anaerobic chamber. Short-term oxygen exposure increases bacterial membrane permeability, without exceeding inter-individual differences. As oxygen exposure remains an important experimental consideration for bacterial metabolism, our data suggest that AnaeroGen sachets are a valid alternative limiting loss of membrane integrity for short-term storage of samples from harder-to-access populations.

Computational Analysis of Microbial Flow Cytometry Data

Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution. The complexity and amount of data necessitate an objective and streamlined data processing workflow that extends beyond commercial instrument software. No full overview of the necessary steps regarding the computational analysis of microbial flow cytometry data currently exists. In this review, we provide an overview of the full data analysis pipeline, ranging from measurement to data interpretation, tailored toward studies in microbial ecology. At every step, we highlight computational methods that are potentially useful, for which we provide a short nontechnical description. We place this overview in the context of a number of open challenges to the field and offer further motivation for the use of standardized flow cytometry in microbial ecology research.

Significance of Viral Activity for Regulating Heterotrophic Prokaryote Community Dynamics along a Meridional Gradient of Stratification in the Northeast Atlantic Ocean

How microbial populations interact influences the availability and flux of organic carbon in the ocean. Understanding how these interactions vary over broad spatial scales is therefore a fundamental aim of microbial oceanography. In this study, we assessed variations in the abundances, production, virus and grazing induced mortality of heterotrophic prokaryotes during summer along a meridional gradient in stratification in the North Atlantic Ocean. Heterotrophic prokaryote abundance and activity varied with phytoplankton biomass, while the relative distribution of prokaryotic subpopulations (ratio of high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) cells) was significantly correlated to phytoplankton mortality mode (i.e., viral lysis to grazing rate ratio). Virus-mediate morality was the primary loss process regulating the heterotrophic prokaryotic communities (average 55% of the total mortality), which may be attributed to the strong top-down regulation of the bacterivorous protozoans. Host availability, encounter rate, and HNA:LNA were important factors regulating viral dynamics. Conversely, the abundance and activity of bacterivorous protozoans were largely regulated by temperature and turbulence. The ratio of total microbial mediated mortality to total available prokaryote carbon reveals that over the latitudinal gradient the heterotrophic prokaryote community gradually moved from a near steady state system regulated by high turnover in subtropical region to net heterotrophic production in the temperate region.

Multi-parametric assessment of biological stability of drinking water produced from groundwater: Reverse osmosis vs. conventional treatment

Although water produced by reverse osmosis (RO) filtration has low bacterial growth potential (BGP), post-treatment of RO permeate, which is necessary prior to distribution and human consumption, needs to be examined because of the potential re-introduction of nutrients/contaminants. In this study, drinking water produced from anaerobic groundwater by RO and post-treatment (ion exchange, calcite contactors, and aeration) was compared with that produced by conventional treatment comprising (dry) sand filtration, pellet softening, rapid sand filtration, activated carbon filtration, and UV disinfection. The multi-parametric assessment of biological stability included bacterial quantification, nutrient concentration and composition as well as bacterial community composition and diversity. Results showed that RO permeate remineralised in the laboratory has an extremely low BGP (50 ± 12 × 10³ ICC/mL), which increased to 130 ± 10 × 10³ ICC/mL after site post-treatment. Despite the negative impact of post-treatment, the BGP of the finished RO-treated water was >75% lower than that of conventionally treated water. Organic carbon limited bacterial growth in both RO-treated and conventionally treated waters. The increased BGP in RO-treated water was caused by the re-introduction of nutrients during post-treatment. Similarly, OTUs introduced during post-treatment, assigned to the phyla of Proteobacteria and Bacteroidetes (75-85%), were not present in the source groundwater. Conversely, conventionally treated water shared some OTUs with the source groundwater. It is clear that RO-based treatment achieved an extremely low BGP, which can be further improved by optimising post-treatment, such as using high purity calcite. The multi-parametric approach adopted in this study can offer insights into growth characteristics including limiting nutrients (why) and dominating genera growing (who), which is essential to manage microbiological water quality in water treatment and distribution systems.

Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes

Polynucleobacter asymbioticus strain QLW-P1DMWA-1^T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection.

Phenotypic heterogeneity as key factor for growth and survival under oligotrophic conditions

Productivity-poor oligotrophic environments are plentiful on earth. Yet it is not well understood how organisms maintain population sizes under these extreme conditions. Most scenarios consider the adaptation of a single microorganism (isogenic) at the cellular level, which increases their fitness in such an environment. However, in oligotrophic environments, the adaptation of microorganisms at population level - that is, the ability of living cells to differentiate into subtypes with specialized attributes leading to the coexistence of different phenotypes in isogenic populations - remains a little-explored area of microbiology research. In this study, we performed experiments to demonstrate that an isogenic population differentiated to two subpopulations under low energy-flux in chemostats. Fluorescence cytometry and turnover rates revealed that these subpopulations differ in their nucleic acid content and metabolic activity. A mechanistic modelling framework for the dynamic adaptation of microorganisms with the consideration of their ability to switch between different phenotypes was experimentally calibrated and validated. Simulation of hypothetical scenarios suggests that responsive diversification upon a change in energy availability offers a competitive advantage over homogenous adaptation for maintaining viability and metabolic activity with time.