A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy

Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth’s microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.

Comment on Trophic strategy and bleaching resistance in reef-building corals

In an era of major environmental changes, understanding corals’ resistance to bleaching is as crucial as it is challenging. A promising framework for inferring corals’ trophic strategies from Stable Isotope Bayesian Ellipses has been recently proposed to this end. As a contribution to this framework, we quantify a risk of bias inherent in its application and propose three alternative adjustments.

Response to Comment on Trophic strategy and bleaching resistance in reef-building corals

Recently, we published a novel method used to assess the trophic niches of different coral species and demonstrated that their nutrition varied considerably, with some species highly dependent on their photosynthetic algal symbionts and others able to feed on plankton to meet energetic requirements. Adjustments to the use of this tool are necessary when it is applied to other scientific questions and symbiotic organisms. We respond to a comment highlighting a risk of bias in the methods, discuss suggested adjustments, and propose further refinements to improve method robustness.

Multi-indicator evidence for habitat use and trophic strategy segregation of two sympatric forms of Arctic char from the Cumberland Sound region of Nunavut, Canada

We analyzed Arctic Char stable isotope ratios and fatty acid composition from two geographically proximal Nunavut lakes, Qasigiyat and Iqalugaarjuit, to determine if anadromous and resident Arctic char occupied different trophic niches. Resident Arctic char had lower δ13C and δ34S, indicative of a freshwater feeding, compared to anadromous individuals. Significantly lower δ15N of residents suggests the ecotypes feed at different trophic levels. Significantly wider δ13C and δ15N ranges in residents implied a broader trophic niche or a wider range in baseline prey isotope values. Results also provide further evidence for resident use of the estuarine environment in Qasigiyat. Immature Arctic char occupy a different trophic niche than both resident and anadromous fish within Iqalugaarjuit, but this relationship is less clear in Qasigiyat. Distinct stable isotope and fatty acid profiles indicate that resident and anadromous Arctic char have distinct trophic niches, marine for anadromous, freshwater for resident. Immature Arctic char seem to occupy a distinct niche from both anadromous and resident fish, which likely relates to use of both freshwater and estuarine environments, depending on developmental stage. We show the first evidence of the fatty acid differences and niche segregation between sympatric anadromous and resident ecotypes in Arctic Char.

Size-related boldness is not altered by stomach flushing in a terrestrial salamander

Animal personality is a relatively neglected field in amphibian research. In this study we assessed the influence of stomach flushing, a non-lethal technique used in amphibian dietary studies, on the boldness behaviour of the cave salamander Speleomantes strinatii. The time of emergence from a shelter located in an unfamiliar environment (a proxy for individual boldness) was measured in 26 cave salamanders before and after stomach flushing, while 14 non-flushed salamanders were tested as controls. Boldness was a repeatable behaviour for salamanders and larger individuals emerged from their shelter more rapidly than smaller ones. Linear mixed model analysis showed that flushing, sex and body condition had no effect on this behaviour. These findings are promising in the framework of the study of salamander personality. In particular, our results will be useful when exploring the relationship between individual trophic strategy and boldness, aggression or exploration behaviours in terrestrial salamanders.

Kleptoplastic foraminifera: a trophic strategy of life

<p>Foraminifera are single-celled organisms, and part of protists. They are present in all types of environments, though most foraminifera are marine benthic and are found from the deep ocean to the intertidal zone. Thus, foraminifera are subjected to various environmental stresses, (natural or anthropogenic). Because of their rapid response to stresses and their strong resistance, foraminifera are studied as paleo-environmental indicators. However, little is currently known about their biology, and specifically their metabolism and physiology. Some foraminifera species are notably known to retain, in their cytoplasm, chloroplasts from diatom preys. This phenomenon is called kleptoplasty. It has been shown that kleptoplasts remain intact and photosynthetically functional from a few days to several weeks, depending of the foraminiferal species and abiotic factors as light. In order to better understand this life strategy and the advantages provided to foraminifera by kleptoplasty in a coastal mudflat environment, we study metabolism of kleptoplastic and non-kleptoplastic species.</p><p>The “Mudsurv” (Mudflat survey, OSUNA) project initiated in 2016 a monitoring of the foraminiferal fauna and sediment geochemistry of Bourgneuf Bay (French Atlantic Coast). The main foraminiferal species observed were: <em>Ammonia sp. </em>T6, <em>Elphidium oceanense</em> and a kleptoplastic specie, <em>Haynesina germanica</em>. We therefore set up a monthly monitoring of respiration and photosynthesis of those kleptoplast and non-kleptoplast foraminifera species. The oxygen production or consumption is measured by microelectrodes in light and darkness. Preliminary results suggest a seasonality of photosynthesis in kleptoplast foraminifera. A second approach, using gas chromatography-mass spectrometry (GC-MS)-based experiments, provided us with the first’s foraminifera metabolomes highlighting kleptoplast species metabolic specificities.</p>

Ecological study based on the distribution of recent foraminifers from southeast of Buenos Aires province, Argentinean Continental Shelf

The study about the distribution of benthic foraminifers in relationship with the type of substrate is presented. Samples of surface sediments from 15 to 60 m of depth from the southeast coast of the province of Buenos Aires (40º 30´ - 42ºS), Argentina were analysed. The foraminiferal assemblage was constituted by forty-eight species that belong to 22 genera. It was characterized mostly by the free-living style, epifaunal microhabitats, oxic levels and a detritivore trophic strategy. Based on statistical analysis, three zones were determinated: at 15 m depth , characterized mainly by Buccella peruviana (d´Orbigny), and species of Bolivina reflected a littoral environment with sandy sediments and the most important clay contribution, whereas it also presented the lowest oxygen levels were determinated; between 24-48 m depth, associted by Ammonia parkinsoniana (d´Orbigny), Buccella peruviana and Quinqueloculina seminula (Linné), this zone displayed an oxygenated environment with coarse grainsize from inner shelf where local water circulation may explain the high energy observed; and the last one located between 36 to 58 m of depth was characterized by Buccella peruviana, Ammonia parkinsoniana, Elphidium macellum (Fichtel & Moll), Cibicides dispars (d´Orbigny) and Cibicides aknerianus (d´Orbigny) regflecting an inner shelf environment with sandy sediments, the lowest water temperature and the highest oxygen levels.

A Midsummer Night’s Diet: Snapshot on Trophic Strategy of the Alpine Salamander, Salamandra atra

Information on the trophic ecology of the Alpine salamander, Salamandra atra, is scattered and anecdotal. We studied for the first time the trophic niche and prey availability of a population from an area located in Italian Dolomites during the first half of August. Considering that S. atra is a typical nocturnal species, we collected food availability separately for diurnal and nocturnal hours. Our aims were: (i) to obtain information on the realized trophic niche; (ii) to provide a direct comparison between trophic strategy considering only nocturnal preys or considering all preys; (iii) to study trophic strategy of this species at the individual level. In two samplings nights we obtained prey from 50 individuals using stomach flushing technique. Trophic strategy was determined using the graphical Costello method and selectivity using the relativized electivity index. During the short timeframe of our sample, this salamander showed a generalized trophic strategy. The total trophic availability differed significantly from nocturnal availability. Interindividual diet variation is discussed in the light of the optimal diet theory. Finally, we highlighted that considering or not the activity time of the studied taxon and its preys may lead to a conflicting interpretation of the trophic strategies.

Trophic strategy and bleaching resistance in reef-building corals

Ocean warming increases the incidence of coral bleaching, which reduces or eliminates the nutrition corals receive from their algal symbionts, often resulting in widespread mortality. In contrast to extensive knowledge on the thermal tolerance of coral-associated symbionts, the role of the coral host in bleaching patterns across species is poorly understood. Here, we applied a Bayesian analysis of carbon and nitrogen stable isotope data to determine the trophic niche overlap between corals and their symbionts and propose benchmark values that define autotrophy, heterotrophy, and mixotrophy. The amount of overlap between coral and symbiont niche was negatively correlated with polyp size and bleaching resistance. Our results indicated that as oceans warm, autotrophic corals lose their competitive advantage and thus are the first to disappear from coral reefs.