Highlights• P-poor soils can affect biological nitrogen fixation (BNF) in several ways.• Nodule bacterial composition was not affected by P deficiency.• However, the nodule metabolic environment was affected.• This caused an alteration in N metabolism the export of N compounds.• Bacterial tolerance to soil P stress may account for host species success. AbstractVirgilia divaricata is an indigenous forest margin legume growing in nutrient richer soils, but it is also known to invade the N and P poorer soils of the mature fynbos, a nutrient-poor ecosystem in the Cape Floristic Region of South Africa. Although this implies that the legume has a wide functional tolerance for variable soil N and P levels, 1 it is not known how the plant utilizes inorganic N under variable P supply. The aim of this experiment was therefore to identify the nodulating bacterial species and their biological N 2 fixing (BNF) efficiencies in V. divaricata during P deficiency.Furthermore, the aim was to integrate plants C and N metabolism to the N product exported via xylem to the shoots. Plants were grown at high and low P levels, both the high and low P plants were then supplied with either 500 µM NH 4 NO 3 as soil nitrogen (N) source or exclusively relied on BNF. Although the bacterial composition of nodules remained seemingly unchanged by P and N supply, the nodule function was greatly altered. In this regard, plants reliant on only N 2 at both P levels had higher and more efficient BNF, which resulted in greater plant N. This may have resulted from two physiological strategies at high and low P, when plants relied only on N 2 fixation.The declines in both sugars and organic acids may imply a reduced energy supply to the bacteroid during P stress. Furthermore altered bacteroid function may be inferred from BNF, and the N compounds synthesized and exported. At high P, plants exported more amino acids relative to inorganic N and ureides in their xylem sap, whereas at low P the plants exported more ureides relative to amino acids and NH 4 . The bacterial tolerance for changes in P and N via nodule metabolites and xylem export might be a major factor that underpins the growth of V. divaricata under these variable soil conditions.

Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological mechanisms that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to environmental perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes recovered from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of these ecosystems. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (non-core) genes showed low in situ coverage based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or ephemeral, 3.49% of them became abundant when salinity (but not light intensity) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results revealed a possible mechanism for how this immense gene diversity is maintained, which has implications for the prokaryotic species concept.

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