Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era.

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.

BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris. RESULTS: The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study. CONCLUSION: Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.

Community characterization of soil from the Central Deccan Plateau dry tropical deciduous forest (Ceddtrof) in central India using 16S rRNA gene amplicon sequencing.

We report a preliminary study of soil from the Central Deccan Plateau dry tropical deciduous forest in India using 16S rRNA gene amplicon sequencing. We report diverse taxa, e.g., Proteobacteria, Actinobacteria, Acidobacteria, Plactomycetes, Chloroflexi, Bacteroidetes, Verrucomicrobia, Gemmatimonadetes, Firmicutes, Crenarchaeota, Nitrospirae, Armatimonadetes, Elusimicrobia, Cyanobacteria, Chlamydiae, Chlorobi, Parvachaeota, Tenericutes, Euryarchaeota, Fibrobacteres, Calditrix, and Spirochaetes.

A new investigation on fractionalized modeling of human liver.

This study focuses on improving the accuracy of assessing liver damage and early detection for improved treatment strategies. In this study, we examine the human liver using a modified Atangana-Baleanu fractional derivative based on the mathematical model to understand and predict the behavior of the human liver. The iteration method and fixed-point theory are used to investigate the presence of a unique solution in the new model. Furthermore, the homotopy analysis transform method, whose convergence is also examined, implements the mathematical model. Finally, numerical testing is performed to demonstrate the findings better. According to real clinical data comparison, the new fractional model outperforms the classical integer-order model with coherent temporal derivatives.

Spatiotemporal variation of microbial communities in surficial sediments of Cochin estuary, southwest coast of India.

Microorganisms play a major role in the degradation of organic matter in sediments. However, the spatiotemporal variation and factors affecting these communities are not clearly understood. At the same time, conventional hydrographic and geochemical parameters do not offer an accurate assessment of transitional ecosystems. PLFA biomarkers which are specific to different taxonomic groups of microorganisms are able to provide a detailed assessment of the community composition in an environment and reflect a more direct assessment of the biological health of transitional ecosystems. We, therefore, conducted a comparison of PLFA biomarkers at four stations (Barmouth, B; Vaduthala, V; Munambam, M; and Arookutty, A) during three seasons (pre-monsoon, PRE; monsoon, MON; and post-monsoon, POST) in the Cochin estuary (CE). Each of the stations represented either a reference point (B), high pollution (V), high salinity (M), or low pollution (A). The communities determined using PLFA profiles could be categorized into six major groups with each group capable of reflecting the state of the ecosystem which correlated with the conventional parameters. The six groups were: G + ve Bacillota (formerly Firmicutes) and G-ve anaerobes (G-I), G-ve aerobic prokaryotes (G-II), ectomycorrhizal fungi (G-III), arbuscular mycorrhizae (G-IV), type-I methanotrophs (G-V), and microeukaryotes (G-VI). The prokaryotes were predominant in sediments amounting to over 78% of the total PLFAs detected, followed by the microeukaryotes. The freshwater-influenced stations were partially anaerobic in nature during PRE and MON and were mainly affected by both marine and terrestrial organic matter inputs, at times prominent in sewage matter. During POST season, CE behaves uniformly, especially in station M. Salinity and DO of BW and texture and organic matter of the sediment were the driving forces for microbial community structure. The reduced presence of cyclopropane fatty acids suggested that the CE was not under any stress during the study period. Our results using PLFA-based community profiling not only provide the fundamental information required to quickly access the impact of stress and other environmental inputs on the CE but also offer a more robust and realistic assessment of the nature of microbial communities in the ecosystem. A periodic and systemic assessment of PLFA profiles at these stations in CE throughout the year will enable the generation of enough metadata enabling a better understanding of this ecosystem and its efficient management in the long term.

Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis.

The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.

Changes in structure and function of bacterial communities during coconut leaf vermicomposting.

To understand bacterial community dynamics during the vermicomposting of lignin-rich coconut leaves using an indigenous isolate of an epigeic earthworm, Eudrilus sp., we employed amplicon-based pyrosequencing of the V1 to V3 region of the 16S rRNA genes. Total community DNA was isolated from two separate vermicomposting tanks in triplicate at four different stages of the process: pre-decomposition (15th day), initial vermicomposting (45th day), 50-70% vermicomposting (75th day) and mature vermicompost (105th day). Alpha diversity measurements revealed an increase in bacterial diversity till the 75th day, which then declined in the mature vermicompost. Beta diversity comparisons showed formation of distinct, stage-specific communities. In terms of relative abundance, the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, Planctomycetes, TM7 and WS3 groups increased until the 50-70% vermicomposting stage (p = 0.05). During the same time, the abundance of Bacteroidetes and Proteobacteria decreased. In contrast, the levels of Firmicutes increased throughout the 105-day vermicomposting process. The distribution of the most abundant OTUs revealed that each stage of the vermicomposting process possessed its own unique microbiome. Predictions based on the OTUs present by PICRUSt suggested a functional shift in the microbiome during vermicomposting. Enzymes and pathways of lipid and lignin metabolism were predicted to be initially abundant, but by the end of the process, biosynthesis of secondary metabolites and plant beneficial properties were enriched. The study revealed that bacterial communities undergo a continuous change throughout the vermicomposting process and that certain OTUs associated with specific stages could be targets for further improvements in the process.

Bacterial Diversity Patterns Differ in Soils Developing in Sub-tropical and Cool-Temperate Ecosystems.

Microbial diversity patterns have been surveyed in many different soils and ecosystems, but we are unaware of studies comparing similar soils developing from similar parent materials in contrasting climates. In 2008, developmental chronosequences with ages ranging from 105 to 500,000 years across Georgia (GA) and Michigan (MI) were studied to investigate how bacterial community composition and diversity change as a result of local environmental gradients that develop during pedogenesis. Geographic factors were studied between and within locations spanning two scales: (1) regionally between 0.1 and 50 and (2) ∼1700 km apart. The diversity was surveyed using high-throughput pyrosequencing, and variance partitioning was used to describe the effects of spatial, environmental, and spatio-environmental factors on bacterial community composition. At the local scale, variation in bacterial communities was most closely related to environmental factors (rM = 0.59, p = 0.0001). There were differences in bacterial communities between the two locations, indicating spatial biogeography. Estimates of bacterial diversity were much greater in MI (numbers of OTU, ACE, and Chao1) and remained 2-3× greater in MI than GA after removing the effect of soil properties. The large differences in diversity between geographically separated bacterial communities in different climates need further investigation. It is not known if the rare members of the community, which contributed to greater bacterial diversity in GA relative to MI, play an important role in ecosystem function but has been hypothesized to play a role in ecosystem resiliency, resistance, and stability. Further research on the link between bacterial diversity and spatial variability related to climate needs further investigation.

K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries.

K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley's K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing.

Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria.

Quorum sensing is known to play a major role in the regulation of secondary metabolite production, especially, antibiotics, and morphogenesis in the phylum Actinobacteria. Although it is one of the largest bacterial phylum, only 25 of the 342 genera have been reported to use quorum sensing. Of these, only nine have accompanying experimental evidence; the rest are only known through bioinformatic analysis of gene/genome sequences. It is evident that this important communication mechanism is not extensively explored in Actinobacteria. In this review, we summarize the different quorum sensing systems while identifying the limitations of the existing screening strategies and addressing the improvements that have taken place in this field in recent years. The γ-butyrolactone system turned out to be almost exclusively limited to this phylum. In addition, methylenomycin furans, AI-2 and other putative AHL-like signaling molecules are also reported in Actinobacteria. The lack of existing screening systems in detecting minute quantities and of a wider range of signaling molecules was a major reason behind the limited information available on quorum sensing in this phylum. However, recent improvements in screening strategies hold a promising future and are likely to increase the discovery of new signaling molecules. Further, the quorum quenching ability in many Actinobacteria has a great potential in controlling the spread of plant and animal pathogens. A systematic and coordinated effort is required to screen and exploit the enormous potential that quorum sensing in the phylum Actinobacteria has to offer for human benefit.

A comparative study of coastal and clinical isolates of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium having a versatile metabolic potential and great ecological and clinical significance. The geographical distribution of P. aeruginosahas revealed the existence of an unbiased genetic arrangement in terrestrial isolates. In contrast, there are very few reports about P. aeruginosa strains from marine environments. The present work was aimed at studying the distribution of P. aeruginosa in coastal waters along the Indian Peninsula and understanding the environmental influence on genotypic, metabolic and phenotypic characteristics by comparing marine and clinical isolates. Of the 785 marine isolates obtained on selective media, only 32 (~4.1%) were identified as P. aeruginosa, based on their fatty acid methyl ester profiles. A low Euclidian distance value (< 2.5) obtained from chemotaxonomic analysis suggested that all the environmental (coastal and marine) isolates originated from a single species. While UPGMA analyses of AP-PCR and phenotypic profiles separated the environmental and clinical isolates, fatty acid biotyping showed overlapping between most clinical and environmental isolates. Our study revealed the genetic diversity among different environmental isolates of P. aeruginosa. While biogeographical separation was not evident based solely on phenotypic and metabolic typing, genomic and metatranscriptomic studies are more likely to show differences between these isolates. Thus, newer and more insightful methods are required to understand the ecological distribution of this complex group of bacteria.

A comparative study of coastal and clinical isolates of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium having a versatile metabolic potential and great ecological and clinical significance. The geographical distribution of P. aeruginosahas revealed the existence of an unbiased genetic arrangement in terrestrial isolates. In contrast, there are very few reports about P. aeruginosa strains from marine environments. The present work was aimed at studying the distribution of P. aeruginosa in coastal waters along the Indian Peninsula and understanding the environmental influence on genotypic, metabolic and phenotypic characteristics by comparing marine and clinical isolates. Of the 785 marine isolates obtained on selective media, only 32 (~4.1%) were identified as P. aeruginosa, based on their fatty acid methyl ester profiles. A low Euclidian distance value (< 2.5) obtained from chemotaxonomic analysis suggested that all the environmental (coastal and marine) isolates originated from a single species. While UPGMA analyses of AP-PCR and phenotypic profiles separated the environmental and clinical isolates, fatty acid biotyping showed overlapping between most clinical and environmental isolates. Our study revealed the genetic diversity among different environmental isolates of P. aeruginosa. While biogeographical separation was not evident based solely on phenotypic and metabolic typing, genomic and metatranscriptomic studies are more likely to show differences between these isolates. Thus, newer and more insightful methods are required to understand the ecological distribution of this complex group of bacteria.

Carl woese: from biophysics to evolutionary microbiology.

This article is a tribute to Carl R. Woese, a biophysicist turned evolutionary microbiologist who passed away on December 30, 2012. We focus on his life, achievements, the discovery of Archaea and contributions to the development of molecular phylogeny. Further, the authors share their views and the lessons learnt from Woese's life with the microbiologists in India. We also emphasize the need for interdisciplinary collaboration and interaction for the progress and betterment of science.

Soil bacterial community succession during long-term ecosystem development.

The physicochemical and biological gradients of soil and vegetative succession along the Franz Josef chrono sequence in New Zealand were used to test whether bacterial communities show patterns of change associated with long-term ecosystem development. Pyrosequencing was conducted on soil-derived 16S rRNA genes at nine stages of ecosystem progression and retrogression, ranging in age from 60 to c. 120 000 years since glacial retreat. Bray­Curtis ordination indicated that the bacterial communities showed clear patterns of change that were closely aligned with ecosystem development, pedogenesis and vegetative succession (Mantel test; r = 0.58; P < 0.001). Eighty per cent (80%) of the explained variability in bacterial community structure was observed during the first c.1000 years of development, when bacterial richness (Simpson's 1/D) declined from 130 to 30. The relatively high turnover of soil bacterial communities corresponded with an integrative 'plant­microbial successional feedback' model that predicts primarily negative feedbacks between plants and soil bacterial communities during progression and early pedogenesis. Positive feedbacks, similar to those of the plant community, could explain the long periods of community stability during later retrogressive stages of ecosystem development. This hypothesized model provides a consistent description linking below ground communities to ecosystem development and succession. The research, using deep sequencing technology, provides the first evidence for soil bacterial community change associated with the process of long-term ecosystem development. How these bacterial community changes are linked to the processes of primary ecosystem succession is not known and needs further investigation.

Microbial cultivation and the role of microbial resource centers in the omics era.

Despite tremendous advances in microbial ecology over the past two decades, traditional cultivation methods have failed to grow ecologically more relevant microorganisms in the laboratory, leading to a predominance of weed-like species in the world's culture collections. In this review, we highlight the gap between culture-based and culture-independent methods of microbial diversity analysis, especially in investigations of slow growers, oligotrophs, and fastidious and recalcitrant microorganisms. Furthermore, we emphasize the importance of microbial cultivation and the acquisition of the cultivation-based phenotypic data for the testing of hypotheses arising from genomics and proteomics approaches. Technical difficulties in cultivating novel microorganisms and how modern approaches have helped to overcome these limitations are highlighted. After cultivation, adequate preservation without changes in genotypic and phenotypic features of these microorganisms is necessary for future research and training. Hence, the contribution of microbial resource centers in the handling, preservation, and distribution of this novel diversity is discussed. Finally, we explore the concept of microbial patenting and requisite guidelines of the "Budapest Treaty" for establishment of an International Depositary Authority.

A variant quorum sensing system in Aeromonas veronii MTCC 3249.

We have investigated the quorum sensing control in Aeromonas veronii MTCC 3249, originally isolated as A. culicicola from the midgut of Culex quinquefasciatus. Based on biosensor assays, the bacterium showed constant production of multiple acyl-homoserine lactones (AHLs) with increasing cell-density. The luxRI gene homologs, acuR (A. culicicola transcriptional Regulator) and acuI (A. culicicola autoInducer) were successfully amplified by inverse-PCR. Sequence analysis indicated acuRI were divergent from all known quorum sensing gene homologs in Aeromonas. Two localized regions in the C-terminal autoinducer binding domain of acuR showed indels suggesting variations in autoinducer specificity. Further, only a single copy of the quorum sensing genes was detected, suggesting a tight regulation of mechanisms under its control. Chromatography and further chemical analysis identified two AHLs in the culture supernatant: 6-carboxy-HHL (homoadipyl homoserine lactone), a novel AHL, and N-tetradecanoylhomoserine lactone. The existence of a potentially variant quorum sensing system might therefore, reflect in some way the ecological strategies adopted by this bacterium in the mosquito midgut.

Transition of microbial communities during the adaption to anaerobic digestion of carrot waste.

In this study a microbial community suitable for anaerobic digestion of carrot pomace was developed from inocula obtained from natural environmental sources. The changes along the process were monitored using pyrosequencing of the 16S rRNA gene. As the community adapted from a diverse natural community to a community with a definite function, diversity decreased drastically. Major bacterial groups remaining after enrichment were Bacilli (31-45.3%), Porphyromonadaceae (12.1-24.8%) and Spirochaetes (12.5-18.5%). The archaeal population was even less diverse and mainly represented by a single OTU that was 99.7% similar to Methanosarcina mazei. One enrichment which failed to produce large amounts of methane had shifts in the bacterial populations and loss of methanogenic archaea.