Beyond the Black Queen Hypothesis

Mas, Alix; Jamshidi, Shahrad; Lagadeuc, Yvan; Eveillard, Damien; Vandenkoornhuyse, Philippe

doi:10.1038/ismej.2016.22

Cited by 109 publications

(112 citation statements)

References 45 publications

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“…What will be the effect of the removal of geographical barriers that have long separated the Earth's biogeographical provinces on marine plankton diversity ("homogocene, " Rosenzweig, 2001)? How does the evolution of microorganism dependency based on gene loss shape the structure and dynamics of communities (Mas et al, 2016)? Due to their fast duplication rates and rapid response to environmental conditions, planktonic communities assemble, dismantle, and re-assemble constantly in natural environments, thus tracking environmental disturbances.…”

Section: Toward a Unified Theory Of Macroecologymentioning

confidence: 99%

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

et al. 2017

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With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modeling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the "Impact of climate change on the distribution of plankton functional and phylogenetic diversity" (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: (1) What can we learn about plankton communities from the new wealth of high-throughput "omics" data? (2) What is the link between plankton diversity and ecosystem function? (3) How can species distribution models be adapted to represent plankton biogeography? (4) How will plankton biogeography be altered due to anthropogenic climate change? and (5) Can a new unifying theory of macroecology be developed based on plankton ecology studies? In this review, we discuss potential future avenues to address these questions, and challenges that need to be tackled along the way.

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Section: Toward a Unified Theory Of Macroecologymentioning

confidence: 99%

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

et al. 2017

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“…Essentially, the theory posits that loss of catalase is favourable in nutrient-limited environments such as the open ocean because (i) catalase is expensive to produce and (ii) its production is redundant if other community members can perform the catalase-enabled function of HOOH removal from seawater. For extended discussions of this theory and its implications in the loss of other microbial functions, the reader is referred to several recent publications (Sachs and Hollowell, 2012;Giovannoni et al, 2014;Oliveira et al, 2014;Fullmer et al, 2015;Morris, 2015;Estrela et al, 2016;Mas et al, 2016).…”

Section: Other Species May Need Cross-protection From Hoohmentioning

confidence: 99%

Cross‐protection from hydrogen peroxide by helper microbes: the impacts on the cyanobacterium Prochlorococcus and other beneficiaries in marine communities

Zinser

2018

Environ Microbiol Rep

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Hydrogen peroxide (HOOH) is a reactive oxygen species, derived from molecular oxygen, that is capable of damaging microbial cells. Surprisingly, the HOOH defence systems of some aerobes in the oxygenated marine environments are critically depleted, relative to model aerobes. For instance, the gene encoding catalase is absent in the numerically dominant photosynthetic cyanobacterium, Prochlorococcus. Accordingly, Prochlorococcus is highly susceptible to HOOH when exposed as pure cultures. Pure cultures do not exist in the marine environment, however. Catalase-positive community members can remove HOOH from the seawater medium, thus lowering the threat to Prochlorococcus and any other member that likewise lacks their own catalase. This cross-protection may constitute a loosely defined symbiosis, whereby the catalase-positive helper cells may benefit through the acquisition of nutrients released by the beneficiaries such as Prochlorococcus. Other members of the community that may be helped by the catalase-positive cells may include some lineages of Synechococcus - the sister genus of Prochlorococcus - as well as some lineages of SAR11 and ammonia oxidizing archaea and bacteria. The co-occurrence of catalase-positive and -negative members suggests that cross-protection from HOOH-mediated oxidative stress may play an important role in the construction of the marine microbial community.

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“…Along these lines, the black queen hypothesis conveys the idea that the loss of a costly gene (cluster) can provide a selective advantage by conserving an organism’s limited resources (Morris et al 2012). Such loss-of-function mutations (e.g abolishing metabolite production) are viable in an environment where other organisms ensure the same function (Mas et al 2016; Morris et al 2012). The black queen hypothesis may at least partially explain the metabolite diversity and high level of cluster loss in the FGSC if different lineages and species frequently co-exist in the same environment or host.…”

Section: Discussionmentioning

confidence: 99%

Complex evolutionary origins of specialized metabolite gene cluster diversity among the plant pathogenic fungi of theFusarium graminearumspecies complex

Tralamazza

Rocha

Oggenfuss

et al. 2019

Preprint

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Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae and F. meridionale). Our analyses of eight species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.

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Beyond the Black Queen Hypothesis

Cited by 109 publications

References 45 publications

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research

Cross‐protection from hydrogen peroxide by helper microbes: the impacts on the cyanobacterium Prochlorococcus and other beneficiaries in marine communities

Complex evolutionary origins of specialized metabolite gene cluster diversity among the plant pathogenic fungi of theFusarium graminearumspecies complex

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