Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages.

Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.

The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance.

BACKGROUND: Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples. RESULTS: Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus. CONCLUSIONS: The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.

Remarkable effects of microbial factors on soil phosphorus bioavailability: A country-scale study.

Low soil phosphorus (P) bioavailability causes the widespread occurrence of P-limited terrestrial ecosystems around the globe. Exploring the factors influencing soil P bioavailability at large spatial scales is critical for managing these ecosystems. However, previous studies have mostly focused on abiotic factors. In this study, we explored the effects of microbial factors on soil P bioavailability of terrestrial ecosystems using a country-scale sampling effort. Our results showed that soil microbial biomass carbon (MBC) and acid phosphatase were important predictors of soil P bioavailability of agro- and natural ecosystems across China although they appeared less important than total soil P. The two microbial factors had a positive effect on soil P bioavailability of both ecosystem types and were able to mediate the effects of several abiotic factors (e.g., mean annual temperature). Meanwhile, we revealed that soil phytase could affect soil P bioavailability at the country scale via ways similar to those of soil MBC and acid phosphatase, a pattern being more pronounced in agroecosystems than in natural ecosystems. Moreover, we obtained evidence for the positive effects of microbial genes encoding these enzymes on soil P bioavailability at the country scale although their effect sizes varied between the two ecosystem types. Taken together, this study demonstrated the remarkable effects of microbial factors on soil P bioavailability at a large spatial scale, highlighting the importance to consider microbial factors in managing the widespread P-limited terrestrial ecosystems.

The widespread capability of methylphosphonate utilization in filamentous cyanobacteria and its ecological significance.

Aquatic ecosystems comprise almost half of total global methane emissions. Recent evidence indicates that a few strains of cyanobacteria, the predominant primary producers in bodies of water, can produce methane under oxic conditions with methylphosphonate serving as substrate. In this work, we have screened the published 2 568 cyanobacterial genomes for genetic elements encoding phosphonate-metabolizing enzymes. We show that phosphonate degradation (phn) gene clusters are widely distributed in filamentous cyanobacteria, including several bloom-forming genera. Algal growth experiments revealed that methylphosphonate is an alternative phosphorous source for four of five tested strains carrying phn clusters, and can sustain cellular metabolic homeostasis of strains under phosphorus stress. Liberation of methane by cyanobacteria in the presence of methylphosphonate occurred mostly during the light period of a 12 h/12 h diurnal cycle and was suppressed in the presence of orthophosphate, features that are consistent with observations in natural aquatic systems under oxic conditions. The results presented here demonstrate a genetic basis for ubiquitous methane emission via cyanobacterial methylphosphonate mineralization, while contributing to the phosphorus redox cycle.

A comprehensive synthesis unveils the mysteries of phosphate-solubilizing microbes.

Phosphate-solubilizing microbes (PSMs) drive the biogeochemical cycling of phosphorus (P) and hold promise for sustainable agriculture. However, their global distribution, overall diversity and application potential remain unknown. Here, we present the first synthesis of their biogeography, diversity and utility, employing data from 399 papers published between 1981 and 2017, the results of a nationwide field survey in China consisting of 367 soil samples, and a genetic analysis of 12986 genome-sequenced prokaryotic strains. We show that at continental to global scales, the population density of PSMs in environmental samples is correlated with total P rather than pH. Remarkably, positive relationships exist between the population density of soil PSMs and available P, nitrate-nitrogen and dissolved organic carbon in soil, reflecting functional couplings between PSMs and microbes driving biogeochemical cycles of nitrogen and carbon. More than 2704 strains affiliated with at least nine archaeal, 88 fungal and 336 bacterial species were reported as PSMs. Only 2.59% of these strains have been tested for their efficiencies in improving crop growth or yield under field conditions, providing evidence that PSMs are more likely to exert positive effects on wheat growing in alkaline P-deficient soils. Our systematic genetic analysis reveals five promising PSM genera deserving much more attention.

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining.

Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.

Field comparison of the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China.

To date, very few attempts have been made to systematically compare the effectiveness of agricultural and nonagricultural organic wastes for aided phytostabilization of mine tailings under field conditions. In this study, we performed a field trial to compare the effectiveness of three agricultural organic wastes: chicken manure (CM), crop straw (CS), and spent mushroom compost (SMC), with that of three nonagricultural organic wastes, municipal sludge (MS), medicinal herb residues (MHR), and sweet sorghum vinasse (SSV) for aided phytostabilization of a Pb-Zn mine tailings pond in Hunan Province, China. Eight plant species naturally established in the vicinity of the mine were selected and seeded onto trial plots. It was found that the CM-amended plots had the highest (p < 0.05) vegetation cover (86%) and biomass production (881 g m-2), compared to other treatments. CM was also one of the best amendments in terms of improving soil nutrient status, increasing activities of soil enzymes, and immobilizing soil Pb. In addition, CM-amended plots were characterized by their higher microbial diversity and distinct microbial community structure as compared to the control plots. MS was the second best amendment in promoting vegetation cover (71%) and biomass production (461 g m-2), and it performed as well as CM for improving nutrient status, immobilizing heavy metals, and increasing the activities of enzymes in the mine tailings. Suggestions for further lines of research are made in order to develop future investigations.

A study on the effects of lead, cadmium and phosphorus on the lead and cadmium uptake efficacy of Viola baoshanensis inoculated with arbuscular mycorrhizal fungi.

The effect of indigenous arbuscular mycorrhizal (AM) fungi on lead (Pb) and cadmium (Cd) uptake by the hyperaccumulator plant Viola baoshanensis was studied in greenhouse pot experiments. Seedlings of V. baoshanensis inoculated without or with indigenous AM fungi were grown in paddy soil with the addition of Pb at 0, 500, 1000 and 1500 mg kg(-1), or of Cd at 0, 50,100, 200 mg kg(-1), or in mine soil with the addition of phosphorus at 0, 50, 250, 500 mg kg(-1). AM colonization increased shoot biomass at low phosphorus levels, and this beneficial effect was diminished or reversed by high phosphorus availability. AM colonization decreased shoot Cd concentrations regardless of the availability of Cd and phosphorus, but the mechanisms involved varied with Cd availability. At low Cd bioavailability, reduced Cd uptake was due to decreased Cd translocation from the roots to the shoots, whereas that was attributed to reduced root uptake at high Cd bioavailability. In contrast, the effect of AM colonization on shoot Pb varied with the availability of phosphorous and Pb. Our results show that the interactions between V. baoshanensis and indigenous AM fungi were modified by the availability of Pb, Cd and phosphorus.

Acidification, heavy metal mobility and nutrient accumulation in the soil-plant system of a revegetated acid mine wasteland.

A revegetation program was established at an extreme acidic and metal-toxic pyrite/copper mine wasteland in Guangdong Province, PR China using a combination of four native grass species and one non-native woody species. It was continued and monitored for 2 y. The emphasis was on acidification, metal mobility and nutrient accumulation in the soil-plant system. Our results showed the following: (i) the acid-forming potential of the mine soils decreased steadily with time, which might be due to plant root-induced changes inhibiting the oxidization of sulphide minerals; (ii) heavy metal extractability (diethylene-triamine-pentaacetic acid-extractable Pb and Zn) in the soils increased with time despite an increase in soil pH, which might be attributed to soil disturbance and plant rhizospheric processes, as well as a consequence of the enhanced metal accumulation in plants over time; and (iii) the vegetation cover increased rapidly with time, and plant development accelerated the accumulation of major nutrients (organic matter, total and ammonium-N, and available P and K). The 2-y field experiment demonstrates that direct seeding/planting of native plant species in combination with lime and manure amelioration is a practical approach to the initial establishment of a self-sustaining vegetation cover on this metalliferous and sulphide-bearing mine wasteland. However, heavy metal accumulation in the soil-plant system should be of great concern, and long-term monitoring of ecological risk must be an integral part of such a restoration scheme.

A transcriptional profile of metallophyte Viola baoshanensis involved in general and species-specific cadmium-defense mechanisms.

Viola baoshanensis Shu, Liu et Lan is a newly identified metallophyte, and its defensive strategies against heavy metals are still unclear. In the present study, we firstly constructed a root cDNA library of the plant subjected to 300muM Cd for 48h by using suppression subtractive hybridization (SSH), and 43 unique cDNA fragments were further isolated from the library. Sequence homology analysis showed that half of the identified genes were involved in general stress defense, such as antioxidative enzymes, protein degradation and stress signal transduction. After RT-PCR and RACE analysis, a Cd-responsive gene Vb40 was identified, which could deduce a novel cysteine-rich mini-protein. Meanwhile, five cyclotide precursor genes (VbCP1-VbCP5) were also identified. The Vb40 and the VbCP1-VbCP5 were further investigated by yeast expression analysis, and they could improve copper (Cu) tolerance in hosted yeast, indicating that these species-specific genes possibly functioned in V. baoshanensis heavy metals tolerance. Our results suggested that heavy metal tolerance in V. baoshanensis relied on both general and species-specific defense.