Impact of grassland afforestation with contrasting tree species on soil phosphorus fractions and alkaline phosphatase gene communities

While grassland afforestation can enhance the net mineralization of soil organic phosphorus (P), the mechanisms involved and impacts of different tree species are not clear. Soil samples were taken from replicated adjacent field plots that had been maintained under unfertilized grazed grassland, radiata pine (Pinus radiata), and eucalyptus (Eucalyptus nitens) for 19 years. Soil phosphorus fractions were determined together with alkaline phosphatase activity and associated phoD and phoX gene analysis. Afforestation significantly decreased soil organic P, microbial biomass P, and soil alkaline phosphatase activity, and increased inorganic P bioavailability, although no differences were measured between radiata pine and eucalyptus. While distinct separation of phoD and phoX gene bacterial communities was associated with afforestation of grassland, separation between tree species was less pronounced. Shifts in phoD and phoX gene community structure were more related to soil moisture and pH than P status. Overall, we found that changes in soil moisture and pH associated with afforestation, rather than tree species per se, significantly affected the occurrence and diversity of bacterial alkaline phosphatase. This highlights the potential effects of changes in land-use and management on soil P dynamics and bioavailability

Validating novel oligonucleotide primers targeting three classes of bacterial non-specific acid phosphatase genes in grassland soils

Background and aims: Microbially driven mineralization of organic phosphorus forms is of particular importance in the soil environment, where it becomes available to plants as inorganic orthophosphates. In acidic soils, microbes produce non-specific acid phosphatases (NSAPs; E.C. 3.1.3.2) which act on the most common forms of organic P in the soil. Our understanding of phosphorus turnover in soils would greatly benefit from an improvement in research tools targeting these genes. Methods: Thus, in this study we developed two novel oligonucleotide PCR primer sets, that will enable researchers to target the present and active communities of bacteria with the genetic potential of acid phosphatase production. A total of three primer sets were validated to target the three classes of NSAPs. Utilizing Illumina MiSeq, amplicons from grassland pasture soils were sequenced. Results: The resulting target specificity was high for all three groups; CAAP (97.2%), CBAP (99.5%), and CCAP (94.8%). Quantification of target genes by qPCR indicated measurable differences between classes, ranging from 5 log to 7.5 log for CAAP, 6 log to 8 log for CBAP, and 4 log to 5 log for CCAP. Conclusions: The validated primer sets were specific to the target genes and identified potential quantitative differences between the NSAP classes

Effect of long-term plant biomass management on phosphatase-producing bacterial populations in soils under temperate grassland

Organic forms of phosphorus (P) account for over half of the total P present in most soils and make a significant contribution to P cycling and plant nutrition through the actions of various plant and microbial phosphatase enzymes. However, not much is known about the bacterial communities harbouring phosphatase genes, either in composition, abundance, or transcriptional activity. Thus a grassland trial was selected that was undergoing long-term management of plant biomass removal/retention. Treatment plots were sampled after 22 years to examine the impact of prolonged nutrient depletion on bacterial communities helping to mediate organic P turnover. Total bacteria, total fungi, alkaline phosphatase (phoD) and the three classes (A, B, C) of non-specific acid phosphatases (NSAPs) were quantified and amplicons of the phoD and NSAP genes were sequenced. Of the genes quantified, class B (CBAP) genes were positively impacted by biomass removal (p < 0.01). Phosphatase gene transcripts generally appeared to increase in the biomass removed plots, but perhaps only weakly differentiated at this one time point. In the removed plots, we identified the class A (CAAP) community as the most significantly differentiated (p < 0.05). This difference was found strongly at the level of the operational taxonomic unit, indicating that changes in composition are reflective of the biomass management. Several key differentiating bacteria were found, many of which shared a closest known identity to Stenotrophomonas spp. Further, Mantel tests also revealed strong associations of NSAP communities CAAP and CCAP to measures of soil biogeochemistry. The findings of this study further support the importance of microbial mediated P cycling and in the contribution of under-studied P cycling enzymes such as bacterial acid phosphatases

Long-term afforestation enhances stochastic processes of bacterial community assembly in a temperate grassland

Afforestation of grassland is being promoted as a measure to mitigate climate change. While grassland afforestation influences the soil bacterial community structure and composition, the mechanisms involved and impacts of different tree species are poorly understood. In this study, we characterized the soil bacterial community to determine the phylogenetic group assembly after 19 years afforestation of unfertilized grazed grassland with radiata pine (Pinus radiata) and eucalyptus (Eucalyptus nitens). The soil bacterial community was more divergent between grassland and forest, while no differences were observed between P. radiata and E. nitens. Dominant roles of homogeneous selection and drift in soil bacterial community assembly were revealed, and comparable community assembly patterns were observed under both tree species. Afforestation increased the relative contribution of stochasticity (particularly drift) by an average of 22 % compared with grassland, and this was primarily associated with Serratia spp. (Gammaproteobacteria). In addition, the relative abundance of drift was significantly correlated with concentrations of plant-available phosphorus and sulfur in soil. These findings advanced understanding of the impact of land-use change on soil bacterial community composition and assembly

Impact of long-term phosphorus fertilizer inputs on bacterial phoD gene community in a maize field, Northeast China

The bacterial phoD gene encodes alkaline phosphomonoesterase, an enzyme which plays an important role in the release of plant-available inorganic phosphorus (P) from organic P in soil. However, the relationships between phoD gene community, alkaline phosphomonoesterase activity, and P availability in soil are poorly understood. In this study, we investigated how alkaline phosphomonoesterase activity, phoD gene abundance, and community structure are influenced by plant-available P using soils (0–10, 10–20 and 20–40 cm) from a long-term field trial in which a continuous maize (Zea mays L.) crop had received different levels of P fertilizer inputs (30, 60 kg P ha⁻¹ year⁻¹) for 28 years. Quantitative PCR and high-throughput sequencing were used to analyze phoD gene abundance and community composition. Alkaline phosphomonoesterase enzyme activity was negatively correlated with soil available P, which was reflected in corresponding data for phoD gene abundance. On the other hand, positive correlations were determined between phoD gene α-diversity and available P, while shifts in phoD gene community structure were related to changes in soil pH and P availability. The relative abundance of Pseudomonas was negatively correlated with P availability and positively correlated with alkaline phosphomonoesterase activity, suggesting that Pseudomonas may play an important role in soil organic P mineralization. The findings of this study demonstrated that changes of soil P availability as a result of long-term P fertilizer inputs significantly affected alkaline phosphomonoesterase activity by regulating phoD gene abundance, diversity, as well as altering the phoD gene community composition

Soil alkaline phosphatase activity and bacterial phoD gene abundance and diversity under long-term nitrogen and manure inputs

The impact of long-term inputs of mineral nitrogen (N) fertilizer and swine manure on soil alkaline phosphatase activity is important for phosphorus (P) availability, although its associated gene abundance and diversity within the soil bacterial community are poorly understood. Topsoil (0–10 cm) samples were taken from triplicate field plots that had been maintained under continuous maize (Zea mays) cropping for 28 years with either no nutrient inputs (control), annual inputs of mineral N (urea), swine manure, or combined mineral N-swine manure. Potential alkaline phosphatase activity was determined, together with phoD gene abundance and diversity that using real-time quantitative polymerase chain reaction (PCR) and high-throughput sequencing. Results showed that potential alkaline phosphatase activity and phoD gene abundance were markedly lower in soil from the mineral N treatment compared with the control. On the other hand, long-term swine manure inputs, with and without mineral N, decreased potential alkaline phosphatase activity and phoD gene abundance compared with the control, although concentrations of plant-available P were higher in manure-amended soils. Distinct separation of phoD gene bacterial communities were associated to each fertilization regime, while less pronounced separation was observed between control and mineral N-swine manure treatments. Furthermore, long-term mineral N and swine manure inputs altered the phoD gene community composition. The relative abundance of Bradyrhizobium was higher in mineral N than control soils, and Pseudomonas was less abundant in swine manure than control soils. Our results indicated that long-term application of mineral N in the absence of P inputs significantly reduced potential alkaline phosphatase activity, abundance and community diversity of phoD gene was attributed to a combination of factors, including a 10-fold increase in soil acidity, decreased soil microbial activity, and the apparent inherent stability of organic P in this soil. The findings of this study demonstrated that long-term mineral N inputs adversely impacted the dynamics and bioavailability of P in soil maintained under continuous cropping

Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand

The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2)