We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.

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UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

Microbes are difficult to culture. Consequently, the primary source of information about a fundamental evolutionary topic, life's diversity, is the environmental distribution of gene sequences. We report the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S rRNA sequences compiled from 111 studies of diverse physical environments. We clustered the samples based on similarities in the phylogenetic lineages that they contain and found that, surprisingly, the major environmental determinant of microbial community composition is salinity rather than extremes of temperature, pH, or other physical and chemical factors represented in our samples. We find that sediments are more phylogenetically diverse than any other environment type. Surprisingly, soil, which has high species-level diversity, has below-average phylogenetic diversity. This work provides a framework for understanding the impact of environmental factors on bacterial evolution and for the direction of future sequencing efforts to discover new lineages.

/pdf/global-patterns-in-bacterial-diversity-1bdp29isp2.pdf

Global patterns in bacterial diversity

Despite the overwhelming bacterial diversity present in the world's oceans, the majority of recognized marine bacteria fall into as few as nine major clades ([36][1]), many of which have yet to be cultivated in the laboratory Molecular-based approaches targeting 16S rRNA genes demonstrate that the

Overview of the marine roseobacter lineage.

Natural products are both a fundamental source of new chemical diversity and an integral component of today's pharmaceutical compendium. Yet interest in natural-product drug discovery has waned, in part owing to diminishing returns from traditional resources such as soil bacteria. The oceans cover 70% of the Earth's surface and harbor most of the planet's biodiversity. Although marine plants and invertebrates have received considerable attention as a resource for natural-product discovery, the microbiological component of this diversity remains relatively unexplored. Recent studies have revealed that select groups of marine actinomycetes are a robust source of new natural products. Members of the genus Salinispora have proven to be a particularly rich source of new chemical structures, including the potent proteasome inhibitor salinosporamide A, and other distinct groups are yielding new classes of terpenoids, amino acid–derived metabolites and polyene macrolides. The continued development of improved cultivation methods and technologies for accessing deep-sea environments promises to provide access to this significant new source of chemical diversity.

Developing a new resource for drug discovery: marine actinomycete bacteria

A comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. Most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. At both poles, the - and -proteobacteria and the Cytophaga-Flavobacterium group were the dominant taxonomic bacterial groups identified by cultivation as well as by molecular methods. The analysis of 16S rRNA gene clone libraries from multiple arctic and antarctic pack ice samples revealed a high incidence of closely overlapping 16S rRNA gene clone and isolate sequences. Simultaneous analysis of environmental samples with fluorescence in situ hybridization (FISH) showed that 95% of 4,6-diamidino-2-phenylindole (DAPI)-stained cells hybridized with the general bacterial probe EUB338. More than 90% of those were further assignable. Approximately 50 and 36% were identified as -proteobacteria in arctic and antarctic samples, respectively. Approximately 25% were identified as -proteobacteria, and 25% were identified as belonging to the Cytophaga-Flavobacterium group. For the quantification of specific members of the sea ice community, new oligonucleotide probes were developed which target the genera Octadecabacter, Glaciecola, Psychrobacter, Marinobacter, Shewanella, and Polaribacter. High FISH detection rates of these groups as well as high viable counts corroborated the overlap of clone and isolate sequences. A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes. Pack ice in the Arctic and Antarctic, with its vast extension and high biological productivity (3, 34, 35, 36, 56), constitutes one of the most significant polar ecosystems. Several similarities exist between the sea ice regimes in the north and the south; however, there are also fundamental differences in formation, development, thickness, maturity, and ice crystal struc

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Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice.

Bacteria in the water beneath the sea ice of the eastern Weddell Sea were homogeneously distributed. Direct counts resembled values from sprmg and autumn, whereas viable cell counts, total ATP concentrations, as well as heterotrophic assimilation and extracellular enzymatic activities were very low, implying a metabolic inactive bactenoplankton The consolidated sea ice had a very heterogeneous horizontal distribution of microbes on large as well as small scales but vertical profiles in low and densely populated ice cores exhibited similar patterns. A close relation between bacterial colonization of sea ice and genetic ice classes was revealed. Sea ice of the 'predominantly congelation ice' had the lowest bacterial biomass and displayed very low heterotrophic activities which were comparable to those of the water column. Samples of older sea ice belonging to the 'mainly frazil' and 'mixed ice' had maximal numbers of bacteria. They often included high proportions of culturable cells and dividing cells as well as large bacteria The bacteria of these ice classes were active and contributed significantly to the productivity in the Weddell Sea during winter 'Predominantly frazil ice' was less colonized; however, selective bacterial growth was also indicated in this typical winter ice by an increase m the proportions of culturable and psychrophihc bacteria with advancing age of the ice Psychrophilic bacteria dominated in consohdated sea-ice whereas facultative psychrophiles prevailed in young sea-ice and water, corroborating a strict partitiomng m a microbial sea-ice and a seawater regime. Generally, temperature does not appear to be the significant factor for the development of bacterial communities in the surface layer of the eastern Weddell Sea m winter smce the metabolically active bacterial flora develops in the very cold sea-ice environment. The organic matter supply and its unproved usabihty obviously controls bacterial activity as well as the selective enrichment of psychrophiles.

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Bacteria in sea ice and underlying water of the eastern Weddell Sea in midwinter

Two groups of nocardioform organisms isolated from marine sediments were studied, along with representative strains of the genera Rhodococcus, Nocardia, and Mycobacterium. Strains of the red- or orange-colored group showed no marine affinity and exhibited a close relationship to Rhodococcus rhodochrous. The 17 marine isolates of the cream-colored group formed a homogeneous well-separated cluster and were particularly characterized as moderately halophilic and psychrotrophic organisms. These isolates were assigned to a new species within the genus Rhodococcus. We propose the name Rhodococcus marinonascens, referring to the exclusive occurrence of this taxon in the sea, and describe the properties of the species and of type strain 3438W (= DSM 43752).

Rhodococcus marinonascens sp. nov., an actinomycete from the sea

The numerical dominance and ecological role of psychrophilic bacteria in bottom sediments, sea ice, surface water and melt pools of the polar oceans were investigated using isolates, colony forming units (CFU) and metabolic activities. All sediment samples of the Southern Ocean studied showed a clear numerical dominance of cold-loving bacteria. In Arctic sediments underlying the influence of cold polar water bodies psychrophiles prevailed also but they were less dominant in sediments influenced by the warm Atlantic Water. A predominance of psychrophiles was further found in consolidated Antarctic sea ice as well as in multiyear Arctic sea ice and in melt pools on top of Arctic ice floes. A less uniform adaptation response was, however, met in polar surface waters. In the very northern part of the Fram Strait (Arctic Ocean) we found bacterial counts and activities at 1°C exceeding those at 22°C. In surface water of the Weddell Sea (Southern Ocean) psychrophiles also dominated numerically in early autumn but the dominance declined obviously with the onset of winter-water and a decrease of chlorphyll a. Otherwise in surface water of the Southern Ocean CFUs were higher at 22°C than at 1°C while activities were vice versa indicating at least a functional dominance of psychrophiles. Even in the temperate sediments of the German Bight true psychrophiles were present and a clear shift towards cold adapted communities in winter observed. Among the polar bacteria a more pronounced cold adaptation of Antarctic in comparison with Arctic isolates was obtained. The results and literature data indicate that stenothermic cold adapted bacteria play a significant role in the global marine environment. On the basis of the temperature response of our isolates from different habitats it is suggested to expand the definition of Morita in order to meet the cold adaptation strategies of the bacteria in the various cold habitats.

Psychrophilic Versus psychrotolerant bacteria: OCcurrence and significance in polar and temperate marine habitats

In the culture broth of the marine Streptomyces sp. B 9173 the two novel diketopiperazines maremycin A (1) and B (2) were detected by chemical screening. Their structures were elucidated and confirmed by the synthesis of the oxindole derivative 4.

H. Weyland

Papers

Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice.

Bacteria in sea ice and underlying water of the eastern Weddell Sea in midwinter

Rhodococcus marinonascens sp. nov., an actinomycete from the sea

Psychrophilic Versus psychrotolerant bacteria: OCcurrence and significance in polar and temperate marine habitats

Marine bacteria, VIII. Maremycin A and B, new diketopiperazines from a marine Streptomyces sp.