Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization

Abstract

BackgroundMany cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus.sp. nov., isolated from the volcanic Lake Albano (Central Italy).ResultsThe novel species Vulcanococcus limneticus sp. nov. falls inside the sub-cluster 5.2, close to the estuarine/marine strains in a maximum-likelihood phylogenetic tree generated with 259 marker genes with representatives from marine, brackish, euryhaline and freshwater habitats. V.limneticus sp. nov. possesses a complete nitrogenase and nif operon. In an experimental setup under nitrogen limiting and non-limiting conditions, growth was observed in both cases. However, the nitrogenase genes (nifHDK) were not transcribed, i.e., V.limneticus sp. nov. did not fix nitrogen, but instead degraded the phycobilisomes to produce sufficient amounts of ammonia. Moreover, the strain encoded many other pathways to incorporate ammonia, nitrate and sulphate, which are energetically less expensive for the cell than fixing nitrogen. The association of the nif operon to a genomic island, the relatively high amount of mobile genetic elements (52 transposases) and the lower observed GC content of V.limneticus sp. nov. nif operon (60.54%) compared to the average of the strain (68.35%) support the theory that this planktonic strain may have obtained, at some point of its evolution, the nif operon by horizontal gene transfer (HGT) from a filamentous or heterocystous cyanobacterium.ConclusionsIn this study, we describe the novel species Vulcanococcus limneticus sp. nov., which possesses a complete nif operon for nitrogen fixation. The finding that in our experimental conditions V.limneticus sp. nov. did not express the nifHDK genes led us to reconsider the actual ecological meaning of these accessory genes located in genomic island that have possibly been acquired via HGT.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4648-3) contains supplementary material, which is available to authorized users.

Ecological and genomic features of two widespread freshwater picocyanobacteria

“…The presence of multiple copies of genes encoding phycocyanin subunits observed in some of the genomes containing type IIB pigmentation (including C. usitatum Tous) may lead to unique light absorption properties and different light adaptations of these strains. Another interesting feature found in the C. usitatum genome is hydrogen synthesis and the apparent regulation of its redox state inside the cell by a bidirectional hydrogenase (HoxHYUFE) and NiFe hydrogenase maturation factor ( hyp ), functions that have been previously observed in other cyanobacteria (Tamagnini et al ., ; Ludwig et al ., ; Di Cesare et al ., ). The abovementioned cyanate hydratase, the PBS clusters and the hydrogenases are all present in genomic islands (see below).…”

“…We detected transport of cobalt, phosphate and sulphonates among many others. Among the flexible genes (category cloud), nitrogenase nif genes were found in the planktonic picocyanobacterium Vulcanococcus limneticus LL (Di Cesare et al, 2018). Other genes associated with the flexible genome encoded many hypothetical proteins, transposases and insertion elements, photosystem subunits, accessory pigments (PBS biosynthesis, allophycocyanin, phycobilin lyases) or chlorophyll biosynthesis.…”

“…However, the enormous diversity of the freshwater genera Synechococcus and Cyanobium is still unexplored at the genomic level. So far, only Synechococcus elongatus (Holtman et al ., ) and a small number of metagenome assembled genomes (MAGs) and draft genomes from different freshwater lakes and reservoirs have been deposited in databases (Bhaya et al ., ; Callieri et al ., ; Shih et al ., ; Guimarães et al ., ; Cabello‐Yeves et al ., , ; Di Cesare et al ., ). The scarcity of metagenomic studies on tropical, temperate, and cold lakes and reservoirs ranging from oligotrophic to eutrophic status, although recently improved, also hampers evaluation of the distribution patterns of freshwater, brackish and euryhaline strains.…”

Nitrogen utilization and transformation ofStenotrophomonas maltophiliaW-6 with nitrogen-fixing ability

“…Moreover, nitrogenase-stabilized gene fragments were also detected by cloning-PCR. These primers were 35F (5′-AAA GGY GGW ATC GGY AAR TCC AC-3′) and 491R (5′-TTG TTS GCS GCR TAC ATS GCC ATC AT-3′) (6,31).…”

On the origin of oxygenic photosynthesis and Cyanobacteria

“…Z denotes a core-bound antenna chlorophyll retained in PSII and Type I reaction centres but lost in the anoxygenic Type II reaction centres concomitant with the loss of core antenna and the evolution of a new light harvesting system. cold extreme habitats(Chrismas et al, 2016;Chrismas et al, 2018); underrepresented freshwater genomes(Di Cesare et al, 2018;S anchez-Baracaldo et al, 2019); and genomes from continental subsurfaces(Puente-S anchez et al, 2018).…”