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Exposing a microbial community to alternating absence and presence of carbon substrate in aerobic conditions is an effective strategy for enrichment of storage polymers (polyhydroxybutyrate, PHB) producing microorganisms. In this work we investigate to which extent intermediate storage polymer production is a temperature independent microbial competition determining factor. Eight parallel bioreactors were operated in the temperature range of 20-40 °C, but intermediate storage polymer production was only obtained at 25-35 °C. Besides PHB production and consumption, cell decay and subsequent cryptic growth on lysis products was found to determine process properties and the microbial community structure at all operational temperatures. At 40 °C decay processes cannot be overcome with additional energy from storage polymers, and fast-growing microorganisms dominate the system. At 20 °C, highly competitive communities with ambiguous storage properties were enriched. The results described here demonstrate that a rigorous experimental approach could aid in the understanding of competitive strategies in microbial communities.

Cooperative behavior is widely spread in microbial populations. An example is the expression of an extracellular protease by the lactic acid bacterium Lactococcus lactis, which degrades milk proteins into free utilizable peptides that are essential to allow growth to high cell densities in milk. Cheating, protease-negative strains can invade the population and drive the protease-positive strain to extinction. By using multiple experimental approaches, as well as modeling population dynamics, we demonstrate that the persistence of the proteolytic trait is determined by the fraction of the generated peptides that can be captured by the cell before diffusing away from it. The mechanism described is likely to be relevant for the evolutionary stability of many extracellular substrate-degrading enzymes. The ISME Journal (2011) 5, 929-932; doi:10.1038/ismej.2010.179; published online 9 December 2010

This data repository contains all data and code needed to rerun the RNA-seq analyses of the paper by Pinseel et al. on salinity acclimation of eight Baltic strains of the ancestrally marine diatom Skeletonema marinoi. Further details can be found in the README-file. Raw sequence reads are available from NCBI's Sequence Read Archive (PRJNA772794). --- Full reference to the paper that describes these data (please reference this study when using any of the data/code published in this Zenodo repository): Pinseel E., Nakov T., Van den Berge K., Downey K.M., Judy K.J., Kourtchenko O., Krempf A., Ruck E.C., Sjöqvist C., Töpel M., Godhe A. & Alverson A.J. (2022) Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. The ISME Journal. doi: 10.1038/s41396-022-01230-x, The A1 publication that describes these data was published in The ISME Journal on April 5th 2022: Pinseel E., Nakov T., Van den Berge K., Downey K.M., Judy K.J., Kourtchenko O., Krempf A., Ruck E.C., Sjöqvist C., Töpel M., Godhe A. & Alverson A.J. (2022) Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. The ISME Journal. doi: 10.1038/s41396-022-01230-x., {"references":["https://doi.org/10.1101/2021.11.04.467364"]}

A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer “culturability” because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A recent paper by Martiny argues that “high proportions” of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer “culturability” because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

A recent paper by Martiny argues that "high proportions" of bacteria in diverse Earth environments have been cultured. Here we reanalyze a portion of the data in that paper, and argue that the conclusion is based on several technical errors, most notably a calculation of sequence similarity that does not account for sequence gaps, and the reliance on 16S rRNA gene amplicons that are known to be biased towards cultured organisms. We further argue that the paper is also based on a conceptual error: namely, that sequence similarity cannot be used to infer "culturability" because one cannot infer physiology from 16S rRNA gene sequences. Combined with other recent, more reliable studies, the evidence supports the conclusion that most bacterial and archaeal taxa remain uncultured.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Bacteriophages are the most abundant biological life forms on Earth. However, relatively little is known regarding which bacteriophages infect and exploit which bacteria. A recent meta-analysis showed that empirically measured phage-bacteria infection networks are often significantly nested, on average, and not modular. A perfectly nested network is one in which phages can be ordered from specialist to generalist such that the host range of a given phage is a subset of the host range of the subsequent phage in the ordering. The same meta-analysis hypothesized that modularity, in which groups of phages specialize on distinct groups of hosts, should emerge at larger geographic and/or taxonomic scales. In this paper, we evaluate the largest known phage-bacteria interaction data set, representing the interaction of 215 phage types with 286 host types sampled from geographically separated sites in the Atlantic Ocean. We find that this interaction network is highly modular. In addition, some of the modules identified in this data set are nested or contain submodules, indicating the presence of multi-scale structure, as hypothesized in the earlier meta-analysis. We examine the role of geography in driving these patterns and find evidence that the host range of phages and the phage permissibility of bacteria is driven, in part, by geographic separation. We conclude by discussing approaches to disentangle the roles of ecology and evolution in driving complex patterns of interaction between phages and bacteria.

Pathogenic bacteria interact not only with the host organism but most probably also with the resident microbial flora. In the knot disease of the olive tree (Olea europaea), the causative agent is the bacterium Pseudomonas savastanoi pv. savastanoi (Psv). Two bacterial species, namely Pantoea agglomerans and Erwinia toletana, which are not pathogenic and are olive plant epiphytes and endophytes, have been found very often to be associated with the olive knot. We identified the chemical signals that are produced by strains of the three species isolated from olive knot and found that they belong to the N-acyl-homoserine lactone family of QS signals. The luxI/R family genes responsible for the production and response to these signals in all three bacterial species have been identified and characterized. Genomic knockout mutagenesis and in planta experiments showed that virulence of Psv critically depends on QS; however, the lack of signal production can be complemented by wild-type E. toletana or P. agglomerans. It is also apparent that the disease caused by Psv is aggravated by the presence of the two other bacterial species. In this paper we discuss the potential role of QS in establishing a stable consortia leading to a poly-bacterial disease.

This is the second paper in a series of three that investigates eukaryotic microbial diversity and taxon distribution in the Cariaco Basin, Venezuela, the ocean's largest anoxic marine basin. Here, we use phylogenetic information, multivariate community analyses and statistical richness predictions to test whether protists exhibit habitat specialization within defined geochemical layers of the water column. We also analyze spatio-temporal distributions of protists across two seasons and two geographic sites within the basin. Non-metric multidimensional scaling indicates that these two basin sites are inhabited by distinct protistan assemblages, an observation that is supported by the minimal overlap in observed and predicted richness of sampled sites. A comparison of parametric richness estimations indicates that protistan communities in closely spaced-but geochemically different-habitats are very dissimilar, and may share as few as 5% of total operational taxonomic units (OTUs). This is supported by a canonical correspondence analysis, indicating that the empirically observed OTUs are organized along opposing gradients in oxidants and reductants. Our phylogenetic analyses identify many new clades at species to class levels, some of which appear restricted to specific layers of the water column and have a significantly nonrandom distribution. These findings suggest many pelagic protists are restricted to specific habitats, and likely diversify, at least in part due to separation by geochemical barriers.

Analyses of archaeal membrane lipids are increasingly being included in ecological studies as a comparatively unbiased complement to gene-based microbiological approaches. For example, crenarchaeol, a glycerol dialkyl glycerol tetraether (GDGT) with a unique cyclohexane moiety, has been postulated as biomarker for ammonia-oxidizing Archaea (AOA). Crenarchaeol has been detected in Nitrosopumilus maritimus and 'Candidatus Nitrosocaldus yellowstonii' representing two of the three lineages within the Crenarchaeota containing described AOA. In this paper we present the membrane GDGT composition of 'Candidatus Nitrososphaera gargensis', a moderately thermophilic AOA, and the only cultivated Group I.1b Crenarchaeon. At a cultivation temperature of 46 degrees C, GDGTs of this organism consisted primarily of crenarchaeol, its regioisomer, and a novel GDGT. Intriguingly, 'Ca. N. gargensis' is the first cultivated archaeon to synthesize substantial amounts of the crenarchaeol regioisomer, a compound found in large relative abundances in tropical ocean water and some soils, and an important component of the TEX(86) paleothermometer. Intact polar lipid (IPL) analysis revealed that 'Ca. N. gargensis' synthesizes IPLs similar to those reported for the Goup I.1a AOA, Nitrosopumilus maritimus SCMI, in addition to IPLs containing uncharacterized headgroups. Overall, the unique GDGT composition of 'Ca. N. gargensis' extends the known taxonomic distribution of crenarchaeol synthesis to the Group I.1b Crenarchaeota, implicating this clade as a potentially important source of crenarchaeol in soils and moderately high temperature environments. Moreover, this work supports the hypothesis that crenarchaeol is specific to all AOA and highlights specific lipids, which may prove useful as biomarkers for 'Ca. N. gargensis'-like AOA.

Our understanding of the composition and activities of microbial communities from diverse habitats on our planet has improved enormously during the past decade, spurred on largely by advances in molecular biology. Much of this research has focused on the bacteria, and to a lesser extent on the archaea and viruses, because of the relative ease with which these assemblages can be analyzed and studied genetically. In contrast, single-celled, eukaryotic microbes (the protists) have received much less attention, to the point where one might question if they have somehow been demoted from the position of environmentally important taxa. In this paper, we draw attention to this situation and explore several possible (some admittedly lighthearted) explanations for why these remarkable and diverse microbes have remained largely overlooked in the present 'era of the microbe'.

Correction to: The ISME Journal (2015) 9, 2153–2161; doi:10.1038/ismej.2015.26; published online 24 April 2015 Since the publication of this paper, the author has noticed an error in the third paragraph of Materials and Methods (under ‘Chemostat reactor operation’). It should read as follows (changes are underlined)

Correction to: The ISME Journal (2015) 9, 2304–2314; doi:10.1038/ismej.2015.98; published online 22 September 2015 Updated online 24 January 2017: This article was originally published under a CC BY-NC-ND 4.0 license, but has now been made available under a CC-BY 4.0 license. The PDF and HTML versions of the paper have been modified accordingly.

Correction to: The ISME Journal 2015; doi: 10.1038/ismej.2015.111 After the publication of this paper, the authors noticed an error in the title. The correct title is ‘Making pathogens sociable: the emergence of high relatedness through limited host invasibility’. The publisher would like to apologise for any inconvenience this may have caused.

A wording error in a sentence in the abstract misrepresented a main finding of the research. The sentence should read: Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community. The sentence has now been corrected. The supplementary file published with the paper was missing figure legends. The correct file is now provided.

Correction to: The ISME Journal (2010) 4, 417–426; doi:10.1038/ismej.2009.127 Since the publication of this paper, the authors have noticed an error in the list of co-authors and affiliations. The correct list of co-authors and affiliations is shown below. Hang Gao1,2,3, Frank Schreiber1, Gavin Collins1,4, Marlene M Jensen1,5, Olivera Svitlica1, Joel E Kostka1,6, Gaute Lavik1, Dirk de Beer1, Huai-yang Zhou2,7 and Marcel MM Kuypers1

Correction to: The ISME Journal (2011) 5, 165–168; doi:10.1038/ismej.2010.81; published online 17 June 2010 Since the publication of this paper, the authors have noticed an omission in their article. The missing text is shown here.

Correction to: The ISME Journal (2010) 6, 777–783; doi:10.1038/ismej.2010.2 Since the publication of this paper, the authors have noticed an omission in the acknowledgements section. The missing text is as follows. LIF, SM and AC were funded by SEP-CONACyT (Mexico), projects no. 56045 (LIF) and 2004-C01-46475-Q (SM, AC), respectively.