Soil enzyme responses to land use change in the tropical rainforest of the Colombian Amazon region

Soil phosphorus cycling across a 100-year deforestation chronosequence in the Amazon rainforest

Deforestation of tropical rainforests is a major land use change that alters terrestrial biogeochemical cycling at local to global scales. Deforestation and subsequent reforestation are likely to impact soil phosphorus (P) cycling, which in P-limited ecosystems such as the Amazon basin has implications for long-term productivity. We used a 100-year replicated observational chronosequence of primary forest conversion to pasture, as well as a 13-year-old secondary forest, to test land use change and duration effects on soil P dynamics in the Amazon basin. By combining sequential extraction and P K-edge X-ray absorption near edge structure (XANES) spectroscopy with soil phosphatase activity assays, we assessed pools and process rates of P cycling in surface soils (0-10 cm depth). Deforestation caused increases in total P (135-398 mg kg-1 ), total organic P (Po ) (19-168 mg kg-1 ), and total inorganic P (Pi ) (30-113 mg kg-1 ) fractions in surface soils with pasture age, with concomitant increases in Pi fractions corroborated by sequential fractionation and XANES spectroscopy. Soil non-labile Po (10-148 mg kg-1 ) increased disproportionately compared to labile Po (from 4-5 to 7-13 mg kg-1 ). Soil phosphomonoesterase and phosphodiesterase binding affinity (Km ) decreased while the specificity constant (Ka ) increased by 83%-159% in 39-100y pastures. Soil P pools and process rates reverted to magnitudes similar to primary forests within 13 years of pasture abandonment. However, the relatively short but representative pre-abandonment pasture duration of our secondary forest may not have entailed significant deforestation effects on soil P cycling, highlighting the need to consider both pasture duration and reforestation age in evaluations of Amazon land use legacies. Although the space-for-time substitution design can entail variation in the initial soil P pools due to atmospheric P deposition, soil properties, and/or primary forest growth, the trend of P pools and process rates with pasture age still provides valuable insights.

Altered activities of extracellular soil enzymes by the interacting global environmental changes

Soil enzymes are crucial in mediating ecosystems' responses to environmental drivers, so that the comprehension of their sensitivity to drivers of global change can help make predictions of future scenarios and design tailored interventions of biomanipulation. Drivers of global change usually act in combination of two or more, and indirect effects of one driver acting through modification of another one often occur, yet most of both manipulative and meta-analysis studies available tend to focus on the direct effect of one single driver on the activity of specific soil enzymes. One of the biggest challenges is, therefore, represented by the difficulty in assessing the interactions between different drivers, due to the complexity of disentangling the single direct effects from the indirect and combined ones. In this review, after elucidating the general mechanisms of soil enzyme production and activity regulation, we display the state-of-the-art knowledge on direct, indirect and combined effects of the main drivers of global change on soil enzyme activities, identify gaps in knowledge and challenges from research, plus we analyse how this can reverberate in the future of biomanipulation techniques for the improvement of ecosystem services. We conclude that qualitative but not quantitative outcomes can be predicted for some interactions such as warming + drought or warming + CO₂ , while for other ones, the results are controversial: future basic research will have to center on this holistic approach. A general trend toward the overall increase of soil enzyme activities and acceleration of biogeochemical cycles will persist, until an inflection will be caused by factors such as future shifts in microbial communities and changes in carbon use efficiency. Applied research will develop toward the refinement of "in situ" analytical systems for the study of soil enzyme activities and the support of bioengineering for the better tailoring of interventions of biomanipulation.

Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils

Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.

Bacteria and Soil Enzymes Supporting the Valorization of Forested Soils

To decompose forest biomass, microorganisms use specific enzymes from the class of oxidoreductases and hydrolases, which are produced by bacteria and soil fungi. In post-agricultural forest soils, bacteria adapt more easily to changing ecological conditions than fungi. The unique features of bacteria, i.e., tolerance and the ability to degrade a wide range of chemical compounds, prompted us to conduct research that contributes to the improvement of the broadly understood circular management of biomass production and economic efficiency. This study aimed to analyze changes in the microbiological activity and the activities of dehydrogenases, catalase, β-glucosidase, urease, arylsulfatase, acid phosphatase, and alkaline phosphatase in the soil sampled from under Picea abies (Pa), Pinus sylvestris (Ps), Larix decidua (Ld), Quercus robur (Qr), and Betula pendula (Bp), after 19 years. The control object was unforested soil. The studies allowed one to demonstrate the relationship between the activity of soil enzymes and the assemblages of culturable microorganisms and bacteria determined by the metagenomic method and tree species. Thus, it is possible to design the selection of tree species catalyzing enzymatic processes in soil. The strongest growth promoter of microorganisms turned out to be Quercus robur L., followed by Picea abies L., whereas the weakest promoters appeared to be Pinus sylvestris L. and Larix decidua M.

Responses of Soil Phosphorus Fractions to Land-Use Change in Colombian Amazon

Intensive land-use change, the overgrazing of pastures, and the poor soil management in the Amazon region induce significant soil chemical degradation, causing alterations in the soil phosphorus (P) dynamics. Here, we studied the changes in P fractions and availability throughout the soil profile along a chronosequence composed of four study areas representing the typical land-use transition from forest to pasture for extensive cattle ranching in the Colombian Amazon region: (i) Forest—Deforested—Pasture 4 years old and Pasture established >25 years after deforestation. Soil samples collected at 0–10, 10–20, 20–30, and 30–40 cm depth were used for the sequential fractionation of P, determination of acid phosphatase activity and soil organic carbon (C) content, and calculation of C:organic P (Po) ratio and P stocks. Our results showed that the land-use change caused a decrease of 31.1% in the fractions of labile inorganic P, with the mineralization of organic P by phosphatase enzyme playing an essential role in the P availability. Although according to the C:Po ratio of the deeper layer the P seems to be sufficient to satisfy the plant needs of all the land uses assessed, the exploitation of soil nutrients in pastures reduced by 6.1% the moderately and non-labile P stock. Given the role of cattle ranching in the economy of tropical countries, it is imperative to adopt strategies of soil P management to improve P-use efficiency, avoiding the degradation of grazing land resources while ensuring the long-term sustainability of rangeland livestock and decrease further deforestation of the Amazon rainforest.