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Studies 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 genes.

Departamento de Biotecnología (INIA), 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 Compet itiveness, the Agencia Estatal de Investigación, and the European Regional Development Fund (grant number AGL2016–80967-R), and Government of Aragon (Research Group A08_20R). The fund ing sources had no involvement in the study design; in the collec tion, analysis and interpretation of data; in the writing of the report; nor in the decision to submit the article for publication, 11Pág.

Special issue Microbial Ecology of Aquatic Systems.-- 17 pages, 5 figures, 1 table, supporting information https://doi.org/10.1111/1462-2920.15835, 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, This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) through the Consolider-Ingenio program (Malaspina 2010 Expedition, CSD2008-00077), with contributions from grants ECLIPSE (PID2019-110128RB-I00) funded to IF, MIAU (RTI2018-101025-B-I00) to JMG and OS, and GRAMMI (RTI2018-099740-J-I00) to Clara RG, all from the Spanish Ministry of Science and Innovation (MICIN). Carlota RG was supported with a contract for research staff training from the Universitat Autònoma de Barcelona. Authors affiliated to the Institut de Ciències del Mar had the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), and IF received the support of the BBVA Foundation through the ‘Becas Leonardo a Investigadores y Creadores Culturales’ 2019 Program. The Foundation takes no responsibility for the contents of this publication, which are entirely the responsibility of its authors. PCJ was supported by São Paulo Research Foundation–FAPESP (PhD grants #2017/26786-1 and #2020/02517-4)