Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans

The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.Versión del edito

Patrones biogeográficos globales de bacterias fotoheterótrofas marinas en la superficie del océano tropical y subtropical

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Candidate genes underlying QTL for flowering time and their interactions in a wide spring barley (Hordeum vulgare L.) cross

Response to vernalization and photoperiod are the main determinants controlling the time to flowering in temperate cereals. While the individual genes that determine a plant's response to these environmental signals are well characterized, the combinatorial effect on flowering time of allelic variants for multiple genes remains unresolved. This study investigated the genetic control of flowering-time in a biparental population of spring barley, derived from a wide cross between a late-flowering European and an early-flowering North-American cultivar. While the major flowering time genes are not segregating in the Beka × Logan cross, large variation in flowering was observed. We identified five QTL, with both parents found to contribute early alleles. The catalog of QTL discovered aligns with several candidate genes affecting flowering time in barley. The combination of particular alleles at HvCEN, HvELF3 and HvFT1 in Logan are responsible for the earliness of this cultivar. Interestingly, earliness for flowering could be further enhanced, with Beka found to contribute three early alleles, including a QTL co-locating with a HvFD-like gene, suggesting that there are diverse aspects of the flowering-time pathway that have been manipulated in these two cultivars. Epistatic interactions between flowering-time QTL or candidate genes were observed in field data and confirmed under controlled conditions. The results of this study link photoperiod-dependent flowering-time genes with earliness per se genes into a single model, thus providing a unique framework that can be used by geneticists and breeders to optimize flowering time in barley.This work was supported by the Spanish Ministry of Economy and Competitiveness (grant numbers AGL2010-21929 and AGL2013-48756-R), the Spanish Ministry of Economy and Competitiveness, the Agencia Estatal de Investigación, and the European Regional Development Fund (grant number AGL2016–80967-R), and Government of Aragon (Research Group A08_20R)

Exploring the diversity of marine photoheterotrophs

2nd Meeting of the Iberian Ecological Society (SIBECOL), 3-8 July 2022, Aveiro, PortugalThe surface ocean is inhabited by a great variety of microorganisms with diverse and versatile metabolisms. Understanding the ecology of marine microbes is of paramount importance since they are essential components of the marine ecosystem, performing key transformations in almost all biogeochemical cycles. A functional group that has attracted the attention of microbial ecologists in the last years is the aerobic anoxygenic phototrophic bacteria, also known as “AAPs”, which are among the few bacterial groups which can use both dissolved organic matter and harvest solar energy for their growth. Their discovery in the surface ocean several years ago, changed the classical conception of bacterioplankton being composed of photoautotrophic microorganisms as primary producers and of chemoheterotrophs as consumers, and forced to rethink the models of organic carbon cycles in the ocean. Since then, AAP bacteria have been studied in diverse marine ecosystems, and at different seasonal scales to understand their ecological role. In this study, we provide the first global assessment of AAP bacterial communities across the tropical and subtropical oceans, using samples collected by the Malaspina Circumnavigation Expedition. By using amplicon sequence variants of the pufM gene, the genetic marker for this functional group, we were able to inspect the composition of AAP communities at a fine scale and describe their diversity and biogeographic patterns. AAP communities in the surface ocean are mainly composed of members of the Halieaceae (Gammaproteobacteria) and different clades of the Alphaproteobacteria, and their distribution changes along gradients of salinity, temperature, and chlorophyll-a concentration. We show that AAP bacteria display their own spatial patterns that largely differ from the observed for the bulk bacterioplankton. Their communities are highly subjected to small changes in environmental conditions and as a result, are dominated by many rare bacteria and habitat specialists. We also show how selection is the main ecological process shaping the structure of their communities. Beyond these results, we have designed and tested new primers to compare the performance of PCRbased approaches, like the one used here, and metagenomics. Using samples from this study and previous ones, we show how the diversity patterns differ when employing different methodologies and discuss the implication of this finding for future studiesPeer reviewe

A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs

12 pages, 3 figures, 1 table, supplementary information https://doi.org/10.1007/s00248-023-02220-y.-- Data Availability: Most of the analyses were performed in R version 4.2.0 (R Core Team 2022), and code is available in the following repository: https://gitlab.com/crgazulla/analysing-pufm-primers-for-marine-aap-studies. The pufM database is available in the Supplementary Material. Amplicon sequences have been deposited in the NCBI Sequence Read Archive (SRA) under BioProject ID PRJNA919028. Sequences from the BBMO metagenomic dataset were published in Auladell et al., [28], and those from the Malaspina Expedition dataset are deposited under BioProject ID PRJEB52452Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genesOpen Access Funding provided by Universitat Autonoma de Barcelona. This work was supported by grant ECLIPSE (PID2019-110128RB-I00/AEI/10.13039/501100011033) funded by the Agencia Estatal de Investigación from the Spanish Ministry of Science and Innovation. Authors affiliated to the Institut de Ciències del Mar received the institutional support of the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S)Peer reviewe

Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans

The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean