Hill number as a bacterial diversity measure framework with high-throughput sequence data

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

BACKGROUND

Connecting the composition and function of industrial microbiomes is a major aspiration in microbial biotechnology. Here, we address this question in wine fermentation, a model system where the diversity and functioning of fermenting yeast species are determinant of the flavor and quality of the resulting wines.

RESULTS

First, we surveyed yeast communities associated with grape musts collected across wine appellations, revealing the importance of environmental (i.e., biogeography) and anthropic factors (i.e., farming system) in shaping community composition and structure. Then, we assayed the fermenting yeast communities in synthetic grape must under common winemaking conditions. The dominating yeast species defines the fermentation performance and metabolite profile of the resulting wines, and it is determined by the initial fungal community composition rather than the imposed fermentation conditions. Yeast dominance also had a more pronounced impact on wine meta-transcriptome than fermentation conditions. We unveiled yeast-specific transcriptomic profiles, leveraging different molecular functioning strategies in wine fermentation environments. We further studied the orthologs responsible for metabolite production, revealing modules associated with the dominance of specific yeast species. This emphasizes the unique contributions of yeast species to wine flavor, here summarized in an array of orthologs that defines the individual contribution of yeast species to wine ecosystem functioning.

CONCLUSIONS

Our study bridges the gap between yeast community composition and wine metabolite production, providing insights to harness diverse yeast functionalities with the final aim to producing tailored high-quality wines. Video Abstract.

Mathematical constraints on a family of biodiversity measures via connections with Rényi entropy

The Hill numbers are statistics for biodiversity measurement in ecological studies, closely related to the Rényi and Shannon entropies from information theory. Recent developments in the mathematics of diversity in the setting of population genetics have produced mathematical constraints that characterize how standard measures depend on the highest-frequency class in a discrete probability distribution. Here, we apply these constraints to diversity statistics in ecology, focusing on the Hill numbers and the Rényi and Shannon entropies. The mathematical bounds can shift perspectives on the diversities of communities, in that when upper and lower bounds on Hill numbers are evaluated in a classic butterfly example, Hill numbers that are initially larger in one community switch positions-so that associated normalized Hill numbers are instead smaller than those of the other community. The new bounds hence add to the tools available for interpreting a commonly used family of statistics for ecological data.

Ubiquitous, B12-dependent virioplankton utilizing ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean

Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B12-dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling-downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral-host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.

Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds

BACKGROUND

In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation.

RESULTS

Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture.

CONCLUSION

The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.

Response of soil bacterial populations to application of biosolids under short-term flooding

Biosolids are applied to agricultural land as a soil conditioner and source of crop nutrients. However, there is concern that bacteria from biosolids may become established in soils, particularly if that soil becomes water-logged. This study examined the microbial community of arable soils cultivated with barley under different applications of biosolids (0, 24t/ha, 48t/ha) in laboratory mesocosms which simulated a 10-day flood. Nutrients (P and N) and organic matter in the soil increased with application rate, but plant growth was not affected by biosolid application. The biosolids contained 10× more genetic material than the soil, with much lower bacterial diversity, yet application did not significantly change the taxonomy of the soil microbiome, with minor changes related to increased nutrients and SOM. Anaerobic conditions developed rapidly during flooding, causing shifts in the native soil microbiome. Some bacterial taxa that were highly abundant in biosolids had slightly increased relative abundance in amended soils during the flood. After flooding, soil bacterial populations returned to their pre-flood profiles, implying that the native microbial community is resilient to transient changes. The short-term changes in the microbiome of biosolid-amended soils during flooding do not appear to increase the environmental risk posed by biosolid application.

Fog-Induced Alteration in Airborne Microbial Community: a Study over Central Indo-Gangetic Plain in India

Fog supports an increase in airborne microbial loading by providing water with nutrients and protecting it from harmful incoming solar radiation. To improve our present understanding of fog-induced alteration in an atmospheric microbial community, a study was conducted during 1 to 14 January 2021 for continuous investigation of airborne bacteria over a rural site, Arthauli (25.95°N, 85.10°E), in central Indo-Gangetic Plain (IGP) in India. An increase of 36% ± 0.4% in airborne bacterial loading was noticed under fog versus prefog conditions, and a decrease of 48% ± 0.4% was noticed under the postfog condition. Airborne bacterial loading had a strong correlation with RH (R2 = 0.56; P < 0.05), temperature (R2 = -0.55, P < 0.05), and wind speed (R2 = -0.52, P < 0.05). Unique types of bacteria, representing about 29% of the whole community, were detected only under foggy conditions, likely by a continuous supply of nutrients and water from a cold, calm, and humid atmosphere. As a result, no significant diurnal variation of bacterial loading was noticed on a foggy day, with a higher daily mean concentration of about (8.4 ± 1.7) × 105 cells · m-3 than that on a typical winter day [(6.3 ± 3.8) × 105 cells · m-3]. A typical winter day experienced about a 60% decrease in bacterial loading in the afternoon in comparison to that in the morning. A 3-day back-trajectory analysis suggests a slow movement of airmass along with the wind blowing from west to central IGP. Fog pauses wind movement, which reduces continuous transportation of urban sources while increasing airborne bacteria from local sources. The abundances of Gp6 (14.8% ± 8.6%), Anaeromyxobacter (7.1% ± 2.8%), and Gp7 (6.8 ± 2.6%) have been observed to increase due to occurrences of fog over central IGP. IMPORTANCE Fog was investigated in the present study as a cause of alteration in the airborne microbial community. Occurrences of fog were responsible for an increase in airborne microbial loading (36%) over central IGP in India due to the easy availability of nutrients and water in the air and dimming of harmful solar radiation. More than 90% of unique bacteria were detected under fog (64%) and postfog (28%) conditions. A few bacteria, like Gp18 (0.5% ± 0.3%), Alicyclobacillus (0.5% ± 0.1%), Sinomonas (0.4% ± 0.2%), and Phenylobacterium (0.4% ± 0.2%), were detected only under foggy conditions. A strong correlation between meteorological parameters and bacterial loading was found in the current research work. The present study provides additional support toward a new direction in interdisciplinary science for the detailed investigations of the effects of meteorological conditions on airborne bacteria and their implications for society.

Effects of Soil Quality on the Microbial Community Structure of Poorly Evolved Mediterranean Soils

Physical and chemical alterations may affect the microbiota of soils as much as the specific presence of toxic pollutants. The relationship between the microbial diversity patterns and the soil quality in a Mediterranean context is studied here to test the hypothesis that soil microbiota is strongly affected by the level of anthropogenic soil alteration. Our aim has been to determine the potential effect of organic matter loss and associated changes in soil microbiota of poorly evolved Mediterranean soils (Leptosols and Regosols) suffering anthropogenic stress (i.e., cropping and deforestation). The studied soils correspond to nine different sites which differed in some features, such as the parent material, vegetation cover, or soil use and types. A methodological approach has been used that combines the classical physical and chemical study of soils with molecular characterization of the microbial assemblages using specific primers for Bacteria, Archaea and ectomycorrhizal Fungi. In agreement with previous studies within the region, physical, chemical and biological characteristics of soils varied notably depending on these factors. Microbial biomass, soil organic matter, and moisture, decreased in soils as deforestation increased, even in those partially degraded to substitution shrubland. Major differences were observed in the microbial community structure between the mollic and rendzic Leptosols found in forest soils, and the skeletic and dolomitic Leptosols in substitute shrublands, as well as with the skeletic and dolomitic Leptosols and calcaric Regosols in dry croplands. Forest soils displayed a higher microbial richness (OTU’s number) and biomass, as well as more stable and connected ecological networks. Here, we point out how human activities such as agriculture and other effects of deforestation led to changes in soil properties, thus affecting its quality driving changes in their microbial diversity and biomass patterns. Our findings demonstrate the potential risk that the replacement of forest areas may have in the conservation of the soil’s microbiota pool, both active and passive, which are basic for the maintenance of biogeochemical processes.

Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats

Due to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on α diversity measurement of soil prokaryotes. Four 1 m² sampling quadrats in a typical grassland were thoroughly surveyed through deep 16S rRNA gene sequencing (over 11 million reads per quadrat) with numerous replicates (33 soil sampling cores with total 141 replicates per quadrat). We found the difference in diversity was relatively small when pooling soil cores before and after DNA extraction and sequencing, but they were both superior to a non-pooling strategy. Pooling a small number of soil cores (i.e., 5 or 9) combined with several technical replicates is sufficient to estimate diversities for soil prokaryotes, and there is great flexibility in pooling original samples or data at different experimental steps. Additionally, the distribution of local α diversity varies with sampling core number, sequencing depth, and abundance distribution of the community, especially for high orders of Hill diversity index (i.e., Shannon entropy and inverse Simpson index). For each grassland soil quadrat (1 m²), retaining 100,000 reads after taxonomic clustering might be a realistic option, as these number of reads can efficiently cover the majority of common species in this area. Our findings provide important guidance for soil sampling strategy, and the general results can serve as a basis for further studies.

Decision-making and best practices for taxonomy-free environmental DNA metabarcoding in biomonitoring using Hill numbers

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km² river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

Hill-based dissimilarity indices and null models for analysis of microbial community assembly

BACKGROUND

High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.

RESULTS

Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.

CONCLUSIONS

Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package ( https://github.com/omvatten/qdiv ). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.

Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical framework for selecting sequencing effort as a function of genome relative abundance. As such, experimental goals in metagenome-assembled genome creation projects can select sequencing effort based on the rarest target genome as a constrained threshold. We hope that the results presented here, as well as GRASE, will be valuable to researchers planning sequencing experiments.

We applied theoretical and simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short-read sequences. First, a coupon collector equation was proposed as an analytical model for predicting sequencing effort as a function of microbial community structure. Characterization was performed by varying community structure properties such as richness, evenness, and genome size. Simulations demonstrated that while community richness and evenness influenced the sequencing effort required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion depended only on the relative abundance of the genome and its genome size. A second analysis evaluated the quantity, completion, and contamination of metagenome-assembled genomes (MAGs) as a function of sequencing effort on four preexisting sequence read data sets from different environments. These data sets were subsampled to various degrees of completeness to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A software tool, Genome Relative Abundance to Sequencing Effort (GRASE), was created to assist investigators to further explore this relationship. Reevaluation of the relationship between sequencing effort and binning success in the context of genome relative abundance, as opposed to base pairs, provides a constraint on sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort.

IMPORTANCE Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical framework for selecting sequencing effort as a function of genome relative abundance. As such, experimental goals in metagenome-assembled genome creation projects can select sequencing effort based on the rarest target genome as a constrained threshold. We hope that the results presented here, as well as GRASE, will be valuable to researchers planning sequencing experiments.

Author Video: An author video summary of this article is available.

Behaviour of carbon-14 containing low molecular weight organic compounds in contaminated groundwater under aerobic conditions

Short chain carbon-14 (¹⁴C) containing organic compounds can be formed by abiotic oxidation of carbides and impurities within nuclear fuel cladding. During fuel reprocessing and subsequent waste storage there is potential for these organic compounds to enter shallow subsurface environments due to accidental discharges. Currently there is little data on the persistence of these compounds in such environments. Four ¹⁴C-labelled compounds (acetate; formate; formaldehyde and methanol) were added to aerobic microcosm experiments that contained glacial outwash sediments and groundwater simulant representative of the Sellafield nuclear reprocessing site, UK. Two concentrations of each electron donor were used, low concentration (10^-5 M) to replicate predicted concentrations from an accidental release and high concentration (10^-2 M) to study the impact of the individual electron donor on the indigenous microbial community in the sediment. In the low concentration system only ∼5% of initial ¹⁴C remained in solution at the end of experiments in contact with atmosphere (250-350 h). The production of ¹⁴CO₂(g) (measured after 48 h) suggests microbially mediated breakdown is the primary removal mechanism for these organic compounds, although methanol loss may have been partially by volatilisation. Highest retention of ¹⁴C by the solid fractions was found in the acetate experiment, with 12% being associated with the inorganic fraction, suggesting modest precipitation as solid carbonate. In the high concentration systems only ∼5% of initial ¹⁴C remains in solution at the end of the experiments for acetate, formate and methanol. In the formaldehyde experiment only limited loss from solution was observed (76% remained in solution). The microbial populations of unaltered sediment and those in the low concentration experiments were broadly similar, with highly diverse bacterial phyla present. Under high concentrations of the organic compounds the abundance of common operational taxonomic units was reduced by 66% and the community structure was dominated by Proteobacteria (particularly Betaproteobacteria) signifying a shift in community structure in response to the electron donor available. The results of this study suggest that many bacterial phyla that are ubiquitous in near surface soils are able to utilise a range of ¹⁴C-containing low molecular weight organic substances very rapidly, and thus such substances are unlikely to persist in aerobic shallow subsurface environments.

Sustained Bauxite Residue Rehabilitation with Gypsum and Organic Matter 16 years after Initial Treatment

Bauxite residue is a high volume byproduct of alumina manufacture which is commonly disposed of in purpose-built bauxite residue disposal areas (BRDAs). Natural waters interacting with bauxite residue are characteristically highly alkaline, and have elevated concentrations of Na, Al, and other trace metals. Rehabilitation of BRDAs is therefore often costly and resource/infrastructure intensive. Data is presented from three neighboring plots of bauxite residue that was deposited 20 years ago. One plot was amended 16 years ago with process sand, organic matter, gypsum, and seeded (fully treated), another plot was amended 16 years ago with process sand, organic matter, and seeded (partially treated), and a third plot was left untreated. These surface treatments lower alkalinity and salinity, and thus produce a substrate more suitable for biological colonisation from seeding. The reduction of pH leads to much lower Al, V, and As mobility in the actively treated residue and the beneficial effects of treatment extend passively 20-30 cm below the depth of the original amendment. These positive rehabilitation effects are maintained after 2 decades due to the presence of an active and resilient biological community. This treatment may provide a lower cost solution to BRDA end of use closure plans and orphaned BRDA rehabilitation.