Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS)

Stepwise degradation of organic matters driven by microbial interactions in China΄s coastal wetlands: Evidence from carbon isotope analysis

The microbial "unseen majority" as drivers of carbon cycle represent a significant source of uncertain climate change. To comprehend the resilience of life forms on Earth to climate change, it is crucial to incorporate knowledge of intricate microbial interactions and their impact to carbon transformation. Combined with carbon stable isotope analysis and high-throughput sequencing technology, the underlying mechanism of microbial interactions for organic carbon degradation has been elucidated. Niche differentiation enabled archaea to coexist with bacteria mainly in a cooperative manner. Bacteria composed of specialists preferred to degrade lighter carbon, while archaea were capable of utilizing heavier carbon. Microbial resource-dependent interactions drove stepwise degradation of organic matter. Bacterial cooperation directly facilitated the degradation of algae-dominated particulate organic carbon, while competitive feeding of archaea caused by resource scarcity significantly promoted the mineralization of heavier particulate organic carbon and then the release of dissolved inorganic carbon. Meanwhile, archaea functioned as a primary decomposer and collaborated with bacteria in the gradual degradation of dissolved organic carbon. This study emphasized microbial interactions driving carbon cycle and provided new perspectives for incorporating microorganisms into carbon biogeochemical models.

Growth rates of marine prokaryotes are extremely diverse, even among closely related taxa

Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, catalyzed reporter deposition fluorescence in situ hybridization subcommunity cell-counts or metagenomic-operational taxonomic units (OTUs). Our calculations unveil a broad range of growth rates (0.3-10 d-1) with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa.

Land use alters bacterial growth dynamics in soil

Microbial growth and mortality are major determinants of soil carbon cycling. We measured in situ growth dynamics of individual bacterial taxa in cropped and successional soils in response to a resource pulse. We hypothesized that land use imposes selection pressures on growth characteristics. We estimated growth and death for 453 and 73 taxa, respectively. The average generation time was 5.04 ± 6.28 (SD; range 0.7-63.5) days. Lag times were shorter in cultivated than successional soils and resource amendment decreased lag times. Taxa exhibiting the greatest growth response also exhibited the greatest mortality, indicative of boom-and-bust dynamics. We observed a bimodal growth rate distribution, representing fast- and slow-growing clusters. Both clusters grew more rapidly in successional soils, which had more organic matter, than cultivated soils. Resource amendment increased the growth rate of the slower growing but not the faster-growing cluster via a mixture of increased growth rates and species turnover, indicating that competitive dynamics constrain growth rates in situ. These two clusters show that copiotrophic bacteria in soils may be subdivided into different life history groups and that these subgroups respond independently to land use and resource availability.

Absolute quantification of viable bacteria abundances in food by next-generation sequencing: Quantitative NGS of viable microbes

Next-generation sequencing (NGS) is an important tool for taxonomical bacteria identification. Recent technological developments have led to its improvement and availability. Despite the undeniable advantages of this approach, it has several limitations and shortcomings. The usual outcome of microbiota sequencing is a relative abundance of bacterial taxa. The information about bacteria viability or enumeration is missing. However, this knowledge is crucial for many applications. In the current study, we elaborated the complete workflow for the absolute quantification of living bacteria based on 16S rRNA gene amplicon sequencing. A fluorescent PMAxx reagent penetrating a damaged cell membrane was used to discriminate between the total and viable bacterial population. Bacteria enumeration was estimated by the spike-in technique or qPCR quantification. For method optimization, twenty bacterial species were taken, and the results of the workflow were validated by widely accepted methodologies: flow cytometry, microbiological plating, and viability-qPCR. Despite the minor discrepancy between all methods used, they all showed compatible results. Finally, we tested the workflow with actual food samples and received a good correlation between the methods regarding the estimation of the number of viable bacteria. Overall, the elaborated and integrated NGS approach could be the next step in perceiving a holistic picture of a sample microbiota.

The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica

The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl₂ L^-1. When grown at a lower concentration of calcium (2 mg CaCl₂ L^-1) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl₂ L^-1 to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls

Marine bacterioplankton represent a diverse assembly of species differing largely in their abundance, physiology, metabolic activity, and role in microbial food webs. To analyze their sensitivity to bottom-up and top-down controls, we performed a manipulation experiment where grazers were removed, with or without the addition of phosphate. Using amplicon-reads normalization by internal standard (ARNIS), we reconstructed growth curves for almost 300 individual phylotypes. Grazer removal caused a rapid growth of most bacterial groups, which grew at rates of 0.6 to 3.5 day⁻¹, with the highest rates (>4 day⁻¹) recorded among Rhodobacteraceae, Oceanospirillales, Alteromonadaceae, and Arcobacteraceae. Based on their growth response, the phylotypes were divided into three basic groups. Most of the phylotypes responded positively to both grazer removal as well as phosphate addition. The second group (containing, e.g., Rhodobacterales and Rhizobiales) responded to the grazer removal but not to the phosphate addition. Finally, some clades, such as SAR11 and Flavobacteriaceae, responded only to phosphate amendment but not to grazer removal. Our results show large differences in bacterial responses to experimental manipulations at the phylotype level and document different life strategies of marine bacterioplankton. In addition, growth curves of 130 phylogroups of aerobic anoxygenic phototrophs were reconstructed based on changes of the functional pufM gene. The use of functional genes together with rRNA genes may significantly expand the scientific potential of the ARNIS technique.

IMPORTANCE Growth is one of the main manifestations of life. It is assumed generally that bacterial growth is constrained mostly by nutrient availability (bottom-up control) and grazing (top-down control). Since marine bacteria represent a very diverse assembly of species with different metabolic properties, their growth characteristics also largely differ accordingly. Currently, the growth of marine microorganisms is typically evaluated using microscopy in combination with fluorescence in situ hybridization (FISH). However, these laborious techniques are limited in their throughput and taxonomical resolution. Therefore, we combined a classical manipulation experiment with next-generation sequencing to resolve the growth dynamics of almost 300 bacterial phylogroups in the coastal Adriatic Sea. The analysis documented that most of the phylogroups responded positively to both grazer removal and phosphate addition. We observed significant differences in growth kinetics among closely related species, which could not be distinguished by the classical FISH technique.

Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile

High-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of the bacteria. We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. To demonstrate the utility of our approach, we quantified the number of bacteria from the compositional data of the fecal and cecal microbiomes. The 16S rRNA gene of a hyperthermophile, Thermus aquaticus, was cloned into Pichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before DNA extraction. 16S rRNA gene library construction and HTS were performed after DNA extraction. The absolute abundances of bacteria were calculated using T. aquaticus reads. The average relative abundances of T. aquaticus in the five stool and five cecal samples were 0.95% and 0.33%, respectively, indicating that the number of bacteria in a cecum sample is 2.9 times higher than that in a stool sample. The method proposed for quantifying the absolute abundance of the bacterial population in this study is expected to overcome the limitation of showing only compositional data in most microbiome studies.

The quest for absolute abundance: The use of internal standards for DNA-based community ecology

To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep

The tolerance of ruminants to gossypol, a natural phenolic compound derived from the cotton plant, is greater than that of monogastric animals, partially because of the gossypol-degrading bacteria in the rumen of the ruminants. In this study, we aimed to examine the effect of gossypol supplementation on fermentation characteristics, bacterial α-diversity and community structure in the rumen fluid of sheep to analyse the change of bacterial in response to gossypol. 8 sheep with permanent fistula were randomly divided into 2 groups, a control and gossypol acetate supplementation groups. Sheep in the latter group were supplemented with gossypol acetate at the levels of 600 mg and 1,200 mg/animal per day during the first (S1, days 1 to 27) and subsequent (S2, days 28 to 47) stages. Gossypol supplementation significantly increased the molar proportion of acetate, and decreased the molar proportion of isobutyric acid, butyric acid, and isovaleric acid in the rumen fluid. Gossypol supplementation have no significant effect on bacterial diversity in the rumen fluid. At the phylum level, gossypol had no effect on bacterial community. At the genus level, gossypol supplementation significantly increased the relative abundance of Treponema_2. However, there were no significant differences in the relative abundance of dominant bacterial genera. In conclusion, gossypol supplementation had an effect on molar proportion of acetate, isobutyric acid, butyric acid, and isovaleric acid, but had no significant effect on the bacterial diversity and relative abundance of dominant bacteria in rumen fluid of sheep.

Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards

Identifying the functional microbes in spontaneous food fermentation is important for improving food quality. To identify the key flavor producers in Chinese liquor fermentation, we propose a novel quantitative microbiome profiling method that uses indigenous internal standards to normalize high-throughput amplicon sequencing results. We screened Lactobacillus acetotolerans and Lactobacillus jinshani as indigenous internal standards based on their high distribution frequencies and relative abundances. After determining the absolute abundance of indigenous internal standards using quantitative PCR with species-specific primers, the liquor-fermented bacterial community and its dynamics were better characterized by internal standards normalization. Based on quantitative microbiome profiling, we identified that Lactobacillus was a key flavor producer correlated with eight flavor compounds. Metatranscriptomic analysis indicated that Lactobacillus was active in transcribing genes involving the biosynthesis of flavor compounds and their precursors. This work has developed a novel and extensible absolute quantification method for microbiota that will alleviate concerns in the statistical analyses based on relative microbiome profiling, and shed insights into the function of Lactobacillus in food fermentation. It can potentially be applied to other microbial ecology studies.IMPORTANCE In this study, we developed a novel strategy using indigenous internal standards to normalize the high-throughput amplicon sequencing results. We chose two Lactobacillus species as indigenous internal standards and characterized the absolute abundance of the bacterial community. Further, we identified Lactobacillus as the key flavor producer using quantitative microbiome profiling combined with multivariate statistics and metatranscriptomic analysis. This work developed a novel strategy for absolute quantitative abundance analysis of microbiota and expanded our understanding of the role of Lactobacillus in food fermentation.

Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations

High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards.

IMPORTANCE High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard

Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3‐V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.

Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria

The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)

Protists are key stone components of aquatic ecosystems, sustaining primary productivity and aquatic food webs. However, their diversity, ecology and structuring factors shaping their temporal distribution remain strongly misunderstood in freshwaters. Using high-throughput sequencing on water samples collected over 16 different months (including two summer and two winter periods), combined with geochemical measurements and climate monitoring, we comprehensively determined the pico- and nanoeukaryotic community composition and dynamics in a Canadian river undergoing prolonged ice-cover winters. Our analysis revealed a large protist diversity in this fluctuating ecosystem and clear seasonal patterns demonstrating a direct and/or indirect selective role of abiotic factors, such as water temperature or nitrogen concentrations, in structuring the eukaryotic microbial community. Nonetheless, our results also revealed that primary productivity, predatory as well as parasitism lifestyles, inferred from fine phylogenetic placements, remained potentially present over the annual cycle, despite the large seasonal fluctuations and the remodeling of the community composition under ice. In addition, potential interplays with the bacterial community composition were identified supporting a possible contribution of the bacterial community to the temporal dynamics of the protist community structure. Our results illustrate the complexity of the eukaryotic microbial community and provide a substantive and useful dataset to better understand the global freshwater ecosystem functioning.

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.