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Sponges accommodate a diverse group of microorganisms with varied metabolic capabilities. The bacterial associates of sponges are widely studied while our understanding of archaeal counterparts is scanty. In the present study, we report the archaeal associates of two sponges, Pseudoceratina purpurea (NCBI barcode: KX454492) and Cinachyra sp. (NCBI barcode: KX454495), found in the coral reef ecosystems of Gulf of Mannar, India. Archaea in the water column was predominated by members of class Halobacteria of Phylum Euryarchaeota (97%) followed by a minor fraction (3%) of Nitrosopumilus sp. of phylum Thaumarchaeota. Interestingly, Thaumarchaeota was identified as the sole archaeal population associated with the two sponges studied, among which Nitrosopumilus sp. occuppied 80 and 100% of the sequences in the clone library of P. purpurea and Cinachyra sp. respectively. Other archaea found in the P. purpurea were Nitrososphaera (10%) and unclassified ones (10%). The study identified Nitrosopumilus sp. as a unique symbiotic archaeon of sponges, P. purpurea and Cinachyra sp. The existence of host driven factors in selecting specific associates from a diverse group of archaea in the environment may need further investigations.

Smut is a serious disease in Job's tears, also known as adlay, and contributes to the reduction of crop yield in agricultural fields. In this study, the key pathogenic fungi in adlay smut disease were first identified by internal transcribed spacer region (ITS) high-throughput sequencing and then used to elucidate the composition and diversity of the fungal community in adlay smut. Results indicate that an abundance of operational taxonomic units (OTUs) were detected in the infected involucres of flowering plants and the OTUs were classified to nine phyla, 20 classes, 45 orders, 90 families and 119 genera. A total of 4 986 OTUs clustered together, sharing six core OTUs in all samples, while 145 OTUs were shared among four geographical groups. The Shannon and Simpson indices ranged from 0.137–1.629 and 0.357–0.970, respectively. Community diversity ranked as Anshun (AS)>Qinglong (QL)>Xingren (XR)>Xingyi (XY) among the four geographical groups by Shannon and Simpson indices, exhibiting complex community diversities among accessions and geographical groups. The richness and diversity data imply a weak relationship between the accession community richness and geographical origins of samples. Two closely related fungal genera, Sporisorium and Ustilago, were implicated as causes of smut disease. The genus Sporisorium appears to be more commonly found among accessions and thus is more likely to be the fungal pathogen causing smut in adlay. This work can facilitate strategies to control and prevent smut infection to improve adlay yield.

Multiple mechanisms collaborate for proper regulation of gene expression. One layer of this regulation is through the clustering of functionally related genes at discrete loci throughout the genome. This phenomenon occurs extensively throughout Ascomycota fungi and is an organizing principle for many gene families whose proteins participate in diverse molecular functions throughout the cell. Members of this phylum include organisms that serve as model systems and those of interest medically, pharmaceutically, and for industrial and biotechnological applications. In this review, we discuss the prevalence of functional clustering through a broad range of organisms within the phylum. Position effects on transcription, genomic locations of clusters, transcriptional regulation of clusters, and selective pressures contributing to the formation and maintenance of clusters are addressed, as are common methods to identify and characterize clusters.

Within the myxomycetes, phylogenetic research is still at a relatively early stage, and available phylogenies are often based on only a single or a few marker genes. According to the available data, the “true” myxomycetes (exosporous, myxogastric) form a monophyletic clade within the phylum Eumycetozoa with two basal subclades, a dark-spored (treated as the Columellomycetidae) and a bright-spored (the subclass Lucisporomycetidae). Within the first subclade the main evolutionary branches are recognized as the orders Echinosteliales, Echinosteliopsidales, Clastodermatales, Meridermatales, Stemonitidales, and Physarales; for the bright-spored subclade, these are the orders Cribrariales, Reticulariales, Liceales, and Trichiales. In the light of molecular data the traditional criteria used in myxomycete taxonomy have to be reevaluated. The morphology of capillitia and peridia, and especially how these two structures are connected to each other in a particular taxon, seems to be highly informative, whereas their presence or absence is not. Similarly, single versus compound fruiting bodies, a character often used to delimit genera, seems to deserve a lower weight, as these structures have evolved several times in parallel. Many, especially species rich, genera seem not to represent monophyletic units, and further research will most likely change their delimitation.

In the mid-1990s, the category ‘Candidatus’ was established for putative taxa of as yet uncultivated prokaryotes. The status of ‘Candidatus’ is not formally included in the rules of the International Code of Nomenclature of Prokaryotes. Thus, ‘Candidatus’ names do not have standing in the nomenclature. Curated annotated lists of ‘Candidatus’ names (not including phyla) have been published since 2020. By April 2021, about 2700 names of ‘Candidatus’ taxa had been published. The International Committee on Systematics of Prokaryotes recently rejected proposals to allow gene sequence data as nomenclatural types. An alternative code for naming uncultivated microorganisms (the ‘SeqCode’) is now being developed for naming the majority of prokaryotes that are as yet uncultivated. In the opinion of the author, there is no need for such a code, as the existing system, with nomenclature quality control also for ‘Candidatus’ names, fulfills the needs. Computer programs such as GAN which generates large numbers of correctly formed names from the short lists of Latin and Greek word elements and Protologger that produce descriptions directly from genome sequences will become important in the future for automated naming and description of large numbers of ‘Candidatus’ taxa from metagenomic and single cell genome data. However, the formation of interesting and meaningful names is encouraged whenever possible.

Summary Accessing enormous uncultivated microorganisms (microbial dark matter) in various Earth environments requires accurate, nondestructive classification, and molecular understanding of the microorganisms in in situ and at the single-cell level. Here we demonstrate a combined approach of random forest (RF) machine learning and single-cell Raman microspectroscopy for accurate classification of phylogenetically diverse prokaryotes (three bacterial and three archaeal species from different phyla). Our RF classifier achieved a 98.8 ± 1.9% classification accuracy among the six species in pure populations and 98.4% for three species in an artificially mixed population. Feature importance scores against each wavenumber reveal that the presence of carotenoids and structure of membrane lipids play key roles in distinguishing the prokaryotic species. We also find unique Raman markers for an ammonia-oxidizing archaeon. Our approach with moderate data pretreatment and intuitive visualization of feature importance is easy to use for non-spectroscopists, and thus offers microbiologists a new single-cell tool for shedding light on microbial dark matter., Graphical abstract, Highlights • Random forest models classify prokaryotic species with high accuracy of >98% • Both bacteria and archaea are classified using minimally preprocessed Raman data • Feature importance reveals what biomolecules contribute to species classification • Raman marker bands for some archaeal species are discovered, Molecular spectroscopy techniques; Microbiology; Machine learning

The data presented in this article are related to the research article entitled “Root-associated community composition and co-occurrence patterns of fungi in wild grapevine”. This dataset documents the diversity of endophytic and rhizoplane fungi found on the roots of 38 wild grapevine plants growing at four locations (Krka, Neretva, Psunj and Paklenica) in Croatia and Bosnia and Herzegovina. We record here 48 identified fungal operational taxonomic units (OTUs) from 3 phyla, 23 families and 30 genera. The material in this Data in Brief paper comprised the data on the identification of OTUs with their corresponding ecological niche, abundance distribution of each fungal OTU recorded in each of the host and location, restrictedness and with fit to the Sloan neutral community model.

Ligninolytic fungi is a large and heterogeneous group of species, mainly from the two phyla Ascomycota and Basidiomycota. They are the main players in the decomposition of wooden materials worldwide. In this chapter, the diversity and distribution of ligninolytic fungal species is presented. Attention is given to how the species diversity can be detected, as fungi are mainly living within their substrate and consequently may be difficult to observe. I present the current knowledge on how the species diversity originates, and the discovery of cryptic ligninolytic fungal species. I also focus on the distribution of ligninolytic fungi, both on how individuals are locally distributed on a single substrate of dead wood and on how species are distributed at larger scales. Across larger scales fungi are affected by the size and environmental conditions in local forests and large-scale climatic variables. The chapter ends with a discussion about conservation, with some perspectives for future research directions.

There is incomplete knowledge of microbial communities available in the domain in relation to treatment using biological wastewater treatment (WWT) reactors due to the limitations of traditional culture-based techniques. A high-density microarray that targets universal 16S rRNA gene can be used to taxonomically recognize a large number of organisms without the use of DNA isolation and sequencing. Microarray-based genomic techniques are powerful tools for viewing thousands of genes expression in single experiment. All investigated microbial communities (as determined by colinearity analysis) with almost identical composition contained a major core of bacterial phyla (53%–82% of 2119 taxa identified). These core species were widely distributed in a very large quantity but their proportions were virtually the same in all samples. The largest phyllum was the Proteobacteria and the subdominant phyla were Firmicutes, Actinobacteria, and Bacteriodetes. The diversity among the samples can be credited solely to a group of operational taxonomic units that were only detected in specific samples. To protect the water environment by removing contaminants from wastewater, an utilization process such as activated sludge or membrane biological reactors is used. This chapter focuses on the microarray-based genomics which are an emerging technology to study microbial communities within biological WWT reactors.

Patterns of community assemblage for plants are associated with particular climatic elements such as water, heat, light, and air. The classification based on these plant assemblages is referred to here as the ecogroup of plants (Eco-Plant), whereas the method of analysing palaeoenvironmental and palaeoclimate variation by using Eco-Plant is called the Eco-Plant model. The online database Sporopollen was created to quickly assign eco-climatic traits to quantitative fossil sporomorph data to assess implications for past vegetation patterns and climatic changes. A user-friendly interface has been created, where users can upload their data to the database and in return get immediate results. This database can automatically link all Mesozoic and Cenozoic sporomorphs to their putative parent plants at phylum, order, or family level. It can also automatically link all Triassic and Jurassic sporomorphs to Eco-Plant groups to assess the effect of humidity (EPH) and the effect of temperature (EPT).•The Eco-Plant model allows to reconstruction of relative Triassic and Jurassic humidity and temperature changes.•A useful tool for palaeoenvironmental reconstruction.•A useful tool for (high-resolution) palynological studies., Graphical abstract Image, graphical abstract

Chytridiomycota is the most species-rich phylum of basal lineage fungi involved in vital processes in both terrestrial and aquatic ecosystems. Still, the diversity and richness of this group remains cryptic. In Northern Europe, few species have been recorded despite the numerous intact lake systems covering this region. Recent classifications of early diverging fungal lineages differ considerably on the diversity of chytrid species and their taxonomic placement. Here, we present the current knowledge of the Chytridiomycota diversity within Northern Europe by using the Global Biodiversity Information Facility (GBIF) data and compare how this diversity distributes across two recently proposed classification systems. Furthermore, we illustrate how various sampling types are influencing the recorded classification levels. Lastly, we discuss how metabarcoding has contributed to the overall understanding of the Chytridiomycota diversity in revealing the “dark matter fungi”, and we point out future research needs in the field of aquatic mycology in the Nordic region. acceptedVersion

Based on the most widely accepted phylogenetic tree of the animal kingdom, the presence or absence of hormones in the phylum is summarized. It seems that hormones emerged originally in cnidarians as paracrine/autocrine neuropeptides in the ring nerve because they have no blood circulatory system. Hormones are also identified in several protostome and deuterostome animals that have no apparent circulatory system. The application of bioinformatics to the genome database enables us to mine possible hormonal peptides and receptors in various animal phyla. Thus, it became evident that almost all hormones and receptors form a family of paralogous genes. With an introduction to this book written by comparative endocrinologists, the author has attempted to summarize the evolutional history and diversity of animals, and to further discuss how hormones have emerged during animal evolution.

The Origin of Chordates has fascinated scientists from the time of Charles Darwin's publication "Descent of Man" in 1871. For over 100 years, it was accepted that chordates evolved from tunicates, our sessile invertebrate sister group. However, genomic and embryonic analyses have shown that lancelets have a body plan and genome much more like vertebrates than do tunicates. In 2000, we proposed a worm-like hypothesis of chordate origins, and genomic and embryonic studies in the past 20 years have supported this hypothesis. This hypothesis contends that the deuterostome ancestor was worm-like, with gill slits, very much like a chordate. In contrast, tunicates have a very derived adult body plan that evolved independently. Here, we review the current understanding of deuterostome phylogeny and supporting evidence for the relationships within each phylum. Then we discuss our hypothesis for chordate origins and evidence to support it. We explore some of the evolutionary changes that ascidians have made to their adult body plan and some of the key gene regulatory networks that have been elucidated in Ciona. Finally, we end with insights that we have gained from studying tailless ascidians for the past 30 years. We've found that differentiation genes, at the end of the gene regulatory networks, become pseudogenes and nonfunctional, even though they are still expressed in tailless ascidians. We expect that eventually these pseudogenes will not be expressed and the ascidian larval body plan is abandoned, leaving the embryo to develop directly into an adult.

Childhood obesity and its consequences are a significant public health problem worldwide. Gut microbiota has a potential role in the development of. In the current datasets, we present 16S rDNA amplicon metasequencing of the gut microbiome of adolescents with normal weight, obesity, and obesity with irritable bowel syndrome (IBS) carried out using the Illumine platform. The datasets presented in this report are partly shown in the research article named "Composition and Structure of Gut Microbiome in Adolescents with Obesity and Different Breastfeeding Duration" [1]. The amplicon metasequencing data were deposited at NCBI SRA as BioProject PRJNA604466. A total of 22 phyla, 34 classes, and 231 genera were revealed. Three groups of adolescents had 196 core amplicon sequence variant (ASV), whereas 45, 24, and 1 ASV were unique for adolescents with normal body weight, obesity, and obesity with IBS, respectively. The metagenomic data were first obtained for adolescents from Eastern Siberian, Russia. They have the potential for predictive analysis, which is crucial for understanding microbial community dynamics and their role in the development of the intestinal microbiome. Considering the recent focus on gut microbiota, new datasets are needed to determine the association between gut microbes and the weight of adolescents from previously unexplored regions such as Siberia, Russia.

High throughput sequencing data collected from acid rock drainage (ARD) communities can reveal the active taxonomic and functional diversity of these extreme environments, which can be exploited for bioremediation, pharmaceutical, and industrial applications. Here, we report a seasonal comparison of a microbiome and transcriptome in Ely Brook (EB-90M), a confluence of clean water and upstream tributaries that drains the Ely Copper Mine Superfund site in Vershire, VT, USA. Nucleic acids were extracted from EB-90M water and sediment followed by shotgun sequencing using the Illumina NextSeq platform. Approximately 575,933 contigs with a total length of 1.54 Gbp were generated. Contigs of at least a size of 3264 (N50) or greater represented 50% of the sequences and the longest contig was 488,568 bp in length. Using Centrifuge against the NCBI “nt” database 141 phyla, including candidate phyla, were detected. Roughly 380,000 contigs were assembled and ∼1,000,000 DNA and ∼550,000 cDNA sequences were identified and functionally annotated using the Prokka pipeline. Most expressed KEGG-annotated microbial genes were involved in amino acid metabolism and several KEGG pathways were differentially expressed between seasons. Biosynthetic gene clusters involved in secondary metabolism as well as metal- and antibiotic-resistance genes were annotated, some of which were differentially expressed, colocalized, and coexpressed. These data can be used to show how ecological stimuli, such as seasonal variations and metal concentrations, affect the ARD microbiome and select taxa to produce novel natural products. The data reported herein is supporting information for the research article “Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site” by Giddings et al. [1] .

Cyanobacteria are photosynthetic bacteria that populate widely different habitats. Accordingly, cyanobacteria exhibit a wide spectrum of lifestyles, physiologies, and morphologies and possess genome sizes and gene numbers which may vary by up to a factor of ten within the phylum. Consequently, large differences exist between individual species in the size and complexity of their regulatory networks. Several non-coding RNAs have been identified that play crucial roles in the acclimation responses of cyanobacteria to changes in the environment. Some of these regulatory RNAs are conserved throughout the cyanobacterial phylum, while others exist only in a few taxa. Here we give an overview on characterized regulatory RNAs in cyanobacteria, with a focus on regulators of photosynthesis, carbon and nitrogen metabolism. However, chances are high that these regulators represent just the tip of the iceberg.

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum., This study was funded by the Max Planck Society, the Spanish Ministry of Science and Innovation and Universities projects CLG2015_66686-C3-1-P and PGC2018-096956-B-C41, both also supported with European Regional Development Fund (FEDER), and the financial support of Deep Blue Sea Enterprise S.L. RMJ would like to thank the Max-Planck-Institute for Marine Microbiology for funding. RRM acknowledges the financial support of the Spanish Ministry through the projects PR2015-00008 and PRX18/00048 for international scientific exchange.

Within the molluscan phylum, the preserved remains of marine bivalves and gastropods in particular may provide important insights into tsunami occurrence and characteristics. This chapter provides an overview of how the taxonomy, taphonomy, and geochemistry of molluscs are helpful for identifying tsunami deposits in onshore and offshore environments worldwide. A comparison of species compositions of molluscan fauna in reported tsunami deposits suggests assemblages are frequently mixed, with species indicative of a range of different source environments. The degree of mixing of different assemblages may be strongly controlled by local topographic features. Taphonomic characteristics reveal additional insights, with tsunami deposits characterized by a high proportion of fractured and fragmented shells, with fewer whole or articulated shells than in other deposits. The identification of allochthonous articulated bivalves that were transported alive by tsunamis enables further insights. Geochemical approaches based on δ18O analysis of these shells may even reveal the season during which a paleotsunami event occurred.

Members of the enigmatic Fusobacteria phylum, once an obscure group, including pathogens primarily of dental and veterinary interest, have recently emerged as contributing features in a range of important chronic diseases in humans, including colorectal cancer (CRC). The fastidious and anaerobic Fusobacterium genus and, in particular, its member species, F. nucleatum, have received the most research attention, which has revealed complex interactions between other member species of the human microbiota, as well as human host cells. Such interactions, particularly in the context of CRC, are of paramount interest to the fields of infectious microbiology and oncology. However, foundational understanding of the basic microbiology, physiology, and function of Fusobacteria is critical, as is an appreciation for the species and strain variability within many genera of this phylum. F. nucleatum, for example, is highly heterogenous and different strains can display quite disparate characteristics. In this chapter, we attempt to summarize the main physiological, phylogenetic, and genotypic attributes of the Fusobacteria, with special emphasis on F. nucleatum.

An updated taxonomic review of Malacostraca from the Neotropical regions is presented in this chapter. Dichotomous identification keys to the lowest justifiable taxonomic level based on the most recent literature are provided. Material preparation methods, defined morphological terms, and current limitations in the knowledge of the group are also presented. Additional information on the “Ecology and General Biology” can be found in Volume I of this book series (Thorp and Rogers, 2015, Elsevier).

The adjective 'Crustata' or Crustacea (L. crusta, hard surface) had been applied by one of the older naturalists, to animals possessing hard skeleton, and Brisson (1756) had used it ‘as the designation of the group'. About 26,000 species of crustaceans have so far been described. These crustaceans inhabit different environments such as marine, freshwater, and terrestrial ones. However, these animals are primarily aquatic, with a majority of species occurring in the marine environment. A large morphological diversity occurs between these crustaceans, and so no one definite criterion describes all crustaceans. When mentioning any criterion, it must be qualified by words such as ‘typically’, ‘usually’, ‘often’, and so on. In addition to the general characteristics that crustaceans attain as arthropods, they can be identified by the following major characteristics: two pairs of antennae, a pair of jaws, and two pairs of maxillae; exoskeleton impregnated with calcium salts; appendages often biramous. This work deals with the embryological development from the formation of gametes to the larva, the Nauplius, which is a mark for the group. Some stress on the sperm, which is not vertebrate sperm, and the formation of the spermatophores are in consideration. Transfer of sperm encapsulated in spermatophores is a common character within the group especially within the decapods. Formation of the larva and its metamorphosis in defferent crustaceans are described.

Biofilms that are formed by a group of pathogenic bacteria and the consequent resistivity against available antimicrobials is the main cause for several chronic and persistent infections. Biofilms have been found to be involved in a wide variety of microbial infections and nearly all types of microbes have the ability to produce biofilms. The phylum actinobacteria is well known as a proliferative source for the production of plethora of bioactive secondary metabolites that have diverse biological activities. Recently, members from this phylum have been looked upon as potential sources of antibiofilm-producing compounds. Moreover, more areas and habitats need to be explored in search of novel compounds and isolates that can fight against antimicrobial-resistant pathogenic strains. This chapter reviews and documents some of the most common bacteria associated with biofilm formation and their pathogenic activities, along with the potential prospects of phylum actinobacteria as natural agent to overcome this problem. There is a need to exploit this phylum to eradicate the biofilm formation potential of many pathogenic bacteria for sustainable development.

In this chapter we present an updated taxonomic review of the inland water members of the phylum Arthropoda, which includes the Chelicerata (mites and spiders), Myriapoda (aquatic millipedes), and Crustacea (crustaceans, apterygotans, and insects). The Chelicerata are covered most extensively in this chapter, while Neotropical insects (now within the subphylum Crustacea) are introduced in Chapter 17 . For extensive coverage of the Neotropical insects, readers are referred to Vol III: Keys to Neotropical Hexapoda. In the current volume, the authors have included sections on taxonomic limitations in the keys, terminology and morphological terms needed to use the keys, techniques for preparing and preserving specimens, and taxonomic keys for spiders and some mite orders, with an emphasis on the oribatid mites.

The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.

Actinobacteria characterize the most important part of the microbial community as they are the sources of novel bioactive compounds. This phylum has the capacity to grow in extreme climatic conditions. Due to their high biotechnological applications, this community has always been a fascinating field of research for chemists, pharmaceutical companies, etc. They are known to produce a wide array of chemically diverse bioactive compounds, such as antibiotics, antitumor and anti-infection agents, and thus open up new possibilities in drug research. In this review, we attempt to highlight the diversity of actinomycetes and their multifaceted role in biotechnology applications.

In this report, the high-throughput sequencing data of soil bacterial communities from indigenous and commercial forests in Tweefontein, South Africa are presented. These data were collected to study the influence of land-use change on soil bacterial diversity and community structure in forests. Illumina Miseq sequencing of 16S rRNA gene amplicon was carried out on soils sampled from Tweefontein commercial (TC) and indigenous (TI) forests in South Africa. The metagenome contained 101,938 sequences with 46,709,377 bp size and 57% G + C content in TI and 91,160 sequences with 41,707,827 bp size and 57% G + C content in TC. Metagenome sequence information are available at NCBI under the Sequence Read Archive (SRA) database with accession numbers SRR8134476 (TI) and SRR8135323 (TC). Taxonomic hits distribution from Metagenomic Rast Server (MG-RAST) analysis of the TI sample revealed the dominance of the phyla Acidobacteria (21.61%), Actinobacteria (18.23%) and Verrucomicrobia (16.78%). Predominant genera were Candidatus Koribacter (12.82%), Candidatus Solibacter (11.74%) and Chthoniobacter (9.36%). MG-RAST assisted analysis of TC sample also detected the dominance of Actinobacteria (23.62%) along with Verrucomicrobia (21.92%) and Acidobacteria (20.74%). Predominant genera were Chthoniobacter (24.94%), Candidatus Solibacter (16.74%) and Candidatus Koribacter (9.39%) which play vital ecological functions in forest ecosystems.

The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession NHRF00000000.

This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks ((5.3±0.6) years old), and 3 elderly yaks ((10.7±0.6) years old), were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units (OTUs). Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera (i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Methanimicrococcus and the unclassified genus) were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacter and Thermogymnomonas, respectively. The abundance of Methanobacteria (class), Methanobacteriales (order), Methanobacteriaceae (family), and Methanobrevibacter (genus) in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Thermogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phylogenetic differences of rumen archaeal structure and composition using the yak model.

Gregarine apicomplexans are closely related to parasites such as Plasmodium, Toxoplasma, and Cryptosporidium, which are causing severe health and economic burdens. Colonizing only invertebrates and having no obvious medical relevance, they are mostly ignored in ‘omics’ studies, although gregarines are the most basal apicomplexans and therefore key players in the understanding of the evolution of parasitism in the Apicomplexa from free-living ancestors. They belong to the only exclusively parasitic phylum of eukaryotes, but is this perception actually true? The effects of gregarines on their hosts seem to cover the whole spectrum of symbiosis from mutualistic to parasitic. We suggest future research directions to understand the evolutionary role of gregarines, by elucidating their biology and interaction with their hosts and the hosts’ microbiota.

Nemerteans, or Ribbon worms as they are sometimes named, may be poorly known to most of us, but nevertheless common in occurence in many habitats. They are active hunters with precise anatomical tools for catching and killing their prey. Although most species are associated to marine environments, they do occur in fresh waters as well as terrestrial. General knowledge of the phylum is available in this chapter.

We summarize the diversity of subterranean-obligate invertebrates and vertebrates that occur in the 48 contiguous United States as well as Hawaii, Alaska, and Canada. These species are found almost exclusively in caves and other subterranean habitats and exhibit some degree of troglomorphy. While a large proportion of the 884 troglobiotic and 469 stygobiotic described species in the United States and Canada are concentrated in 10 biogeographic karst regions, significant diversity exists in other karst and also nonkarst terrain, and new biogeographic regions may be recognized in the future. This diversity includes 5 phyla, 15 classes, 51 orders, 124 families, and 288 genera. Nearly 150 new species have been described since 2008 and many additional taxa await formal description. More than 70% of troglobiont and stygobionts in the United States and Canada are of conservation concern and at an elevated risk of extinction.

The diversity and abundance of aromatic compounds in nature is crucial for proper metabolism in all biological systems, and also impacts greatly the development of many industrial processes. Naturally, understanding their catabolism becomes fundamental for many scientific fields of research, from clinical and environmental to technological. The genetic basis of the central pathways for the catabolism of aromatic compounds in fungi, particularly of benzene derivatives, remains however poorly understood largely overlooking their significance. In some Dikarya species the genes of the central pathways are clustered in the genome, often in an array with peripheral pathway genes, even if the existence of a specific pathway does not necessarily mean that the composing genes are clustered. The current availability of many annotated fungal genomes in the postgenomic era creates conditions to reach a more holistic view of these processes through target analysis of the central pathways gene clusters. Inspired by this, we have critically analyzed the established biochemical and genetic data on the catabolism of aromatic compounds in Dikarya after dissecting the presence and distribution of central catabolic gene clusters (at times including also details on gene diversity, order and orientation) and of peripheral genes. Our methodological approach illustrates the multiple degrees of separation in these central pathways gene clusters across Dikarya. Surprisingly, they show a great degree of similarity irrespectively of the Dikarya division, emphasizing that knowledge established on either phyla can guide the identification of clusters of comparable composition (in-cluster plus peripheral genes) in uncharacterized species.

Extremophiles, especially alkaliphiles, are the group of microorganisms growing optimally at or above pH 9. These organisms have been isolated from various alkaline niches such as soda lakes, soda deserts, etc. Out of those, Rift Valley, Wadi Natrun, and Lonar Lake are extensively studied. The microorganisms found are adapted to these alkaline habitats through pH homeostasis in which various cell membrane proteins are involved. Many researchers throughout the globe have explored these extreme habitats for isolation of novel alkaliphiles, alkalithermophiles belonging to various phyla such as Firmicutes, Gammaproteobacteria, Actinobacteria, Archaea, etc. Advancement in molecular biology technique leads to study diversity by culture independent methods such as metagenomics and genome sequencing. Many novel phyla described through this process are Cytophaga/Flavobacterium/Bacteroides, Planctomycetes, Cyanobacteria, Spirochaeta, etc. This vast diversity of alkaliphiles harbors a great biotechnological potential in production of industrially important enzymes, antibiotics, exopolysaccharides, and polyhydroxyalkanoates. Thus, one has to conserve these pristine habitats to preserve the wealth of microbes in future.

Echinoderms are important research models for a wide range of biological questions. In particular, echinoderm embryos are exemplary models for dissecting the molecular and cellular processes that drive development and testing how these processes can be modified through evolution to produce the extensive morphological diversity observed in the phylum. Modern attempts to characterize these processes depend on some level of genomic analysis; from querying annotated gene sets to functional genomics experiments to identify candidate cis-regulatory sequences. Given how essential these data have become, it is important that researchers using available datasets or performing their own genome-scale experiments understand the nature and limitations of echinoderm genomic analyses. In this chapter we highlight the current state of echinoderm genomic data and provide methodological considerations for common approaches, including analysis of transcriptome and functional genomics datasets.

In the present study, it was ascertained whether dietary fibre preparations derived from potato starch with prebiotic properties would promote the growth of Bacteroidetes strains while also inhibiting Firmicutes strains at the same time. The fibre preparations were added to faecal samples from obese children and incubated for 24 hours at 37 °C under anaerobic conditions. It was found that the studied preparations stimulate the growth of bacterial strains belonging to the phyla Bacteroidetes and Actinobacteria, while reducing the quantity of strains belonging to the phylum Firmicutes – especially Clostridium (enzyme-resistant citric acid-modified dextrin D1 p = 0.02, enzyme-resistant tartaric acid-modified dextrin D2 p

The application of sewage sludge to agricultural soil induces co-exposure of prokaryotic populations to antibiotics and heavy metals, thus exerting a selection pressure that may lead to the development of antibiotic resistance. Here, soil samples from a long-term factorial field experiment in which sewage sludge was applied to agricultural soil, at different rates (40 and 80 t ha(-1)) and frequencies (every 1, 2 and 4 years) of application, were studied to assess: (i) the effect of sewage sludge application on prokaryotic community composition, (ii) the links between prokaryotic community composition and antibiotic resistance profiles, and (iii) the links between antibiotic resistance and metal(oid) concentrations in amended soil. We found no significant impact of sewage sludge on prokaryotic community composition. Some antibiotic resistance genes (ARGs) correlated positively with particular prokaryotic taxa, being Gemmatimonadetes the taxon with the greatest number of positive correlations at phylum level. No positive correlation was found between prokaryotic taxa and genes encoding resistance to sulfonamides and FCA. All metal(oid)s showed positive correlations with, at least, one ARG. Metalloid) concentrations in soil also showed positive correlations with mobile genetic element genes, particularly with the gene tnpA-07. These data provide useful information on the links between soil prokaryotic composition and resistome profiles, and between antibiotic resistance and metal(oid) concentrations, in agricultural soils amended with sewage sludge. (C) 2018 The Authors. Published by Elsevier Inc. This work was supported by the by the Basque Government through URAGAN project. The first author was the recipient of a predoctoral fellowship from the Department for Economic Development and Infrastructures of the Basque Government. The authors thank for technical and human support provided by SGIker of UPV/EHU and European funding (ERDF and ESF).

The genus Sinomonas is a Gram-staining positive, non-motile bacteria that belongs to the family Micrococcaceae of the phylum Actinobacteria. In this chapter, we cover various characters of Sinomonas species, such as its present taxonomic placement, species ecological niche, and morphological, physiological, biochemical, chemotaxonomic, and molecular characters. Interestingly, members of this genus have been revealed as a valuable source for important enzymes and plant growth promoters. They have been reported for synthesizing silver nanoparticles, increasing fuel efficacy, and for bioremediation. The genus is less known among the phylum Actinobateria, but has good bioactivity and energy value. Hence, new ecological niche, together with selective isolation techniques, has to be designed to explore their valuable sources.

Actinobacteria is a phylum of gram-positive bacteria, and members of bacteria belonging to this phylum are classified into six classes, namely Acidimicrobiia, Actinobacteria, Coriobacteriia, Nitriliruptoria, Rubrobacteria, and Thermoleophilia. Among the six different classes, members of the actinobacteria class are the most dominant and contain one of the largest genera, Streptomyces, with 961 distinct species. Members of phylum actinobacteria are ubiquitous in nature and have been isolated from various extreme environments (high temperatures, pH, salinities, pressure, and drought) and are associated with plants growing in different habitats. The rhizospheric actinobacteria are the most dominant in nature and they are of great economic importance to humans due to their huge contributions to soil systems. Based on a comprehensive literature analysis members of phylum actinobacteria have been reported from different genera such as Acidimicrobium, Actinomyces, Arthrobacter, Bifidobacterium, Cellulomonas, Clavibacter, Corynebacterium, Frankia, Microbacterium, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, Pseudonocardia, Rhodococcus, Sanguibacter, and Streptomyces. Actinobacteria can be utilized as bioinoculants for sustainable agriculture as they can enhance plant growth and yield both by directly promoting plant growth by the fixation of atmospheric nitrogen, the solubilization of minerals such as phosphorus, potassium, and zinc, the production of siderophores and plant growth hormones such cytokinin, auxin, and gibberellins, and by indirect plant growth promotion via production of antagonistic substances by inducing resistance against plant pathogens. The actinobacteria has been proved to have immense importance in biotechnological applications in various industrial and agricultural processes that are discussed in this chapter.

Penicillium, a filamentous fungus, is a large genus that is important economically, ecologically, and medically. Conventionally, fungi are identified by their macro- and micromorpho-physiological characteristics. An often tedious, ambiguous, and time-consuming method that may take up to 8 weeks or more under ideal culture conditions is needed to observe the different life-cycle stages of a sample with compulsory optimization of techniques. Additionally such methods require an even more skilled professional to deduce the phylum, genus, or even species of the sample fungus as many diverse fungi have similar characteristics. Molecular methods are the most definitive for identifying fungi. The sequence of specific DNA has been used as the basis for molecular-based identification, including ribosomal RNA (rRNA), the second largest ribosomal subunit of RNA polymerase II. The four ribosomal rRNA genes, the 26 to 28S, 18S, 5.8S, and 5S genes, are arranged as head-to-tail tandem repeats separated by the spacer regions, which include the internal transcribed spacer region useful for classification. For these techniques, isolation, amplification, and sequencing of purified DNA fragment are necessary. These sequences are further analyzed by bioinformatic tools. The fungal species are then determined based on the sequence results submitted to the National Center for Biotechnology Information, Basic Local Alignment Search Tool program for alignment with highly similar sequences. New state-of-the-art techniques in sequencing (next-generation) offer valuable tools in both detection of mycobiota and in understanding the molecular mechanisms. Introduction of new sequencing platforms with enhanced capacity and a reduction in costs for sequence analysis provides a potential and powerful tool in mycological diagnosis and research. In this chapter, we focus on the applications of next-generation sequencing techniques to study the diversity of Penicillium species.

Due to similarities between members of the genera Bifidobacterium and Lactobacillus , historically the taxonomy of these organisms has often been confused; indeed, many former and contemporary texts have addressed these genera together. A major factor for this intermixing is that both taxa share several morphological and physiological similarities; for example, both are Gram-stain positive, are nonspore-forming and produce significant amounts of lactic acid as end-products of glucose metabolism. Furthermore, both Bifidobacterium and Lactobacillus are regularly isolated from the GI tract of human infants and adults and both genera have been associated with potential health-promoting properties. However, several important traits can be used to differentiate between these taxa, the DNA mol.% G + C of bifidobacteria is much higher than lactobacilli and, in addition, the metabolic hexose bifidum shunt containing the key enzyme fructose-6-phosphate phosphoketolase are unique to the genus Bifidobacterium . But, it was not until the advent of molecular methods, and most significantly the application of 16S and 23 rRNA gene sequencing, that the taxonomy of these groups was finally resolved. Not only were the two genera found to be well separated, but more extraordinary, were phylogenetically located in different phyla; Lactobacillus was located within the Firmicutes while Bifidobacterium was found to be placed within the Actinobacteria . The phylum Actinobacteria is one of the major phyla in the domain Bacteria and is based on the branching pattern in the 16S rRNA gene tree and taxon-specific 16S rRNA signatures. This is further supported by the presence of conserved insertions and deletions (or indels) in certain proteins, and characteristic gene rearrangements. Within the phylum six classes have been circumscribed: Actinobacteria, Acidimicrobidiia, Coriobacteria, Nitriliruptoria, Rubrobacteria , and Thermoleophilia .

Sandy-beach invertebrate communities are usually dominated by annelids, mollusks, and crustaceans in the intertidal zone and by insects and crustaceans in the supralittoral, around and above the drift line. The orders, families, and genera typical of these groups on sandy shores are introduced, with brief notes on their biology. Numerous other phyla are also covered, including Cnidaria, Platyhelminthes, Nemertea, Nematoda, Echiurida, Sipunculida, Brachiopoda, Echinodermata, and Hemichordata.

Sexual and asexual reproduction in the phylum Playthelminthes (flatworms) are described. The early separation of the ovary into germarium and vitellarium is highlighted and the chemistry of quinone-tanning of the eggshell and modes of hatching are considered. There is confusion in the literature concerning the naming and function of the germarium, ootype, uterus, penis and cirrus. The roles of these organs in cross-insemination and self-insemination are clarified. Hypodermic impregnation, ovoviviparity and viviparity are explored, as are the production of spermatophores and the role of pseudospermatophores.

The human immune system is a complex assembly of innate (i.e., germline encoded) and adaptive (i.e., somatically generated) mechanisms. Among Metazoa, invertebrates use mostly innate mechanisms, whereas vertebrates have maximized the usage of somatic mechanisms, allowing each individual to adapt to the changing pathogenic environment. Historically, Metazoa have developed immune systems from a limited number of shared elements, hence the homologies observed between phyla (e.g., in the conservation of some signaling cascades). The different immune systems of Metazoa offer also examples of analogies that reflect the intensity of the selection pressures. Analogies in diversifying immunoreceptors are the most striking.

Actinobacteria isolated from freshwater has become an emerging area in the field of microbiology for its untapped bio-resources including secondary metabolites production. The phylum actinobacteria has been reported as prolific producers of thousands of bioactive secondary metabolites. Among the phylum, the genus Streptomyces is considered as one of the most dominant genus in freshwater, accounting for the production of more than 50% of the total known bioactive natural compounds. Since most of the researchers working on freshwater habitats are concerned with the diversity of actinobacteria, literature regarding the production of secondary metabolites from freshwater actinobacteria remains scarce and very little information is known about their ecological role in freshwater ecosystems. Freshwater with reference to actinobacteria has been relatively neglected and largely unexplored. So the search for actinobacteria in these regions is of significant interest for the discovery of novel compounds. This chapter highlights the significance of freshwater actinobacteria by evaluating the work done by various researchers on actinobacteria in various freshwater sources, which covers the isolation, media used for the isolation, their antimicrobial potential, and the metabolites synthesized. With the increase in multiple drug resistant diseases, there come greater demands for new biologically active compounds synthesized by actinobacteria from freshwater sources.

RNA-Seq was used to examine the microbial, eukaryotic, and viral communities in water catchments (‘tanks’) formed by tropical bromeliads from Costa Rica. In total, transcripts with taxonomic affiliation to a wide array of bacteria, archaea, and eukaryotes, were observed, as well as RNA-viruses that appeared related to the specific presence of eukaryotes. Bacteria from 25 phyla appeared to comprise the majority of transcripts in one tank (Wg24), compared to only 14 phyla in the other (Wg25). Conversely, eukaryotes from only 16 classes comprised the majority of transcripts in Wg24, compared to 24 classes in the Wg25, revealing a greater eukaryote diversity in the latter. Given that these bromeliads had tanks of similar size (i.e. vertical oxygen gradient), and were neighboring with presumed similar light regime and acquisition of leaf litter through-fall, it is possible that pH was the factor governing these differences in bacterial and eukaryotic communities (Wg24 had a tank pH of 3.6 and Wg25 had a tank pH of 6.2). Archaeal diversity was similar in both tanks, represented by 7 orders, with the exception of Methanocellales transcripts uniquely recovered from Wg25. Based on measures of FPKG (fragments mapped per kilobase of gene length), genes involved in methanogenesis, in addition to a spirochaete flagellin gene, were among those most highly expressed in Wg25. Conversely, aldehyde dehydrogenase and monosaccharide-binding protein were among genes most highly expressed in Wg24. The ability to observe specific presence of insect, plant, and fungi-associated RNA-viruses was unexpected. As with other techniques, there are inherent biases in the use of RNA-Seq, however, these data suggest the possibility of understanding the entire community, including ecological interactions, via simultaneous analysis of microbial, eukaryotic, and viral transcripts.

Planctomycetes are a unique divergent phylum of the domain Bacteria. Members display a number of unusual properties, such as cell compartmentalization among many species examined electron microscopically, the presence of unusual or unique lipids, such as sterols and ladderane lipids in some species, and unique physiology in some species, such as the anammox planctomycetes performing ammonium oxidation anaerobically. This chapter will outline their diversity, examine planctomycete cell compartmentalization as a new model for cell complexity and activities, and outline the potential of planctomycete species to be considered significant new microbial resources, including sources for new lipids and enzymes, and for new types of waste remediation technology on industrial scales utilizing the anammox process unique to planctomycetes.

Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.

Egg pigmentation is proposed to serve numerous ecological, physiological, and adaptive functions in egg-laying animals. Despite the predominance and taxonomic diversity of egg layers, syntheses reviewing the putative functions and drivers of egg pigmentation have been relatively narrow in scope, centring almost exclusively on birds. Nonvertebrate and aquatic species are essentially overlooked, yet many of them produce maternally provisioned eggs in strikingly varied colours, from pale yellow to bright red or green. We explore the ways in which these colour patterns correlate with behavioural, morphological, geographic and phylogenetic variables in extant classes of Echinodermata, a phylum that has close phylogenetic ties with chordates and representatives in nearly all marine environments. Results of multivariate analyses show that intensely pigmented eggs are characteristic of pelagic or external development whereas pale eggs are commonly brooded internally. Of the five egg colours catalogued, orange and yellow are the most common. Yellow eggs are a primitive character, associated with all types of development (predominant in internal brooders), whereas green eggs are always pelagic, occur in the most derived orders of each class and are restricted to the Indo-Pacific Ocean. Orange eggs are geographically ubiquitous and may represent a 'universal' egg pigment that functions well under a diversity of environmental conditions. Finally, green occurs chiefly in the classes Holothuroidea and Ophiuroidea, orange in Asteroidea, yellow in Echinoidea, and brown in Holothuroidea. By examining an unprecedented combination of egg colours/intensities and reproductive strategies, this phylum-wide study sheds new light on the role and drivers of egg pigmentation, drawing parallels with theories developed from the study of more derived vertebrate taxa. The primary use of pigments (of any colour) to protect externally developing eggs from oxidative damage and predation is supported by the comparatively pale colour of equally large, internally brooded eggs. Secondarily, geographic location drives the evolution of egg colour diversity, presumably through the selection of better-adapted, more costly pigments in response to ecological pressure.

This is the first report on the metagenomic approach for unveiling the microbial diversity of Lasundra hot spring, Gujarat State, India. High-throughput sequencing of community DNA was performed on an Ion Torrent PGM platform. Metagenome consisted of 606,867 sequences represent 98,567,305bps size with an average length of 162bps and 46% G+C content. Metagenome sequence information is available at EBI under EBI Metagenomic database with accession no. ERP009313. MG-RAST assisted community analysis revealed that 99.21% sequences were bacterial origin, 0.43% was fit to eukaryotes and 0.11% belongs to archaea. A total of 29 bacterial, 20 eukaryotic and 4 archaeal phyla were detected. Abundant genera were Bacillus (86.7%), Geobacillus (2.4%), Paenibacillus (1.0%), Clostridium (0.7%) and Listeria (0.5%), that represent 91.52% in metagenome. In functional analysis, Cluster of Orthologous Group (COG) based annotation revealed that 45.4% was metabolism connected and 19.6% falls in poorly characterized group. Subsystem based annotation approach suggests that the 14.0% was carbohydrates, 7.0% was protein metabolism and 3.0% genes for various stress responses together with the versatile presence of commercially useful traits.