Microbial Diversity of Reconstituted, Degraded, and Agricultural Soils Assessed by 16S rDNA Multi-Amplicon Sequencing

The microbial diversity is, among soil key factors, responsible for soil fertility and nutrient biogeochemical cycles, and can be modified upon changes in main soil physicochemical properties and soil pollution. Over the years, many restoration techniques have been applied to restore degraded soils. However, the effect of these approaches on soil microbial diversity is less understood and thus requires more investigation. In this study, we analyzed the impact, on soil microbial diversity of a patented novel technology, used to restore degraded soils. Soil samples were collected from three nearby sites located in Borgotrebbia, Piacenza, Italy, and categorized as reconstituted, degraded, and agricultural soils. After total soil DNA extraction, 16S rDNA multi-amplicon sequencing was carried out using an Ion GeneStudio S5 System to compare soils’ bacterial community profiles. Sequenced reads were processed to assign taxonomy and then key microbial community differences were identified across the sampling sites. Species diversity featured significant abatement at all rank levels in the degraded soil when compared to the agricultural control. The 5 year restoration technique showed full recovery of this index at the genus level but not at the phylum level, displaying a rank-dependent gradient of restored richness. In parallel, the abundance of genes involved in the nitrogen (N) biogeochemical cycle was assessed using quantitative Real-Time PCR (qPCR). Total DNA content was significantly higher (p < 0.05) in degraded (μ = 12.69 ± 2.58 μg g−1) and reconstituted (μ = 11.73 ± 1.65 μg g−1) soil samples when compared to the agricultural soil samples (μ = 2.39 ± 0.50 μg g−1). The taxonomic diversity of each soil site was significantly different, with some instances unique of the agricultural soil even at the phylum level. The analysis of N functional genes showed that the relative abundance of bacterial amoA (p < 0.05) and nosZ (p < 0.01) genes were significantly lower in the agricultural than in the reconstituted and degraded soils. We concluded that the application of the soil reconstitution technique appears to enhance the active microbial community, with distinct diversity and functionality towards genes involved in N biogeochemical cycle, as compared to both the degraded and the agricultural soil.

Substantial accumulation of mercury in the deepest parts of the ocean and implications for the environmental mercury cycle

Anthropogenic activities have led to widespread contamination with mercury (Hg), a potent neurotoxin that bioaccumulates through food webs. Recent models estimated that, presently, 200 to 600 t of Hg is sequestered annually in deep-sea sediments, approximately doubling since industrialization. However, most studies did not extend to the hadal zone (6,000- to 11,000-m depth), the deepest ocean realm. Here, we report on measurements of Hg and related parameters in sediment cores from four trench regions (1,560 to 10,840 m), showing that the world’s deepest ocean realm is accumulating Hg at remarkably high rates (depth-integrated minimum–maximum: 24 to 220 μg ⋅ m−2 ⋅ y−1) greater than the global deep-sea average by a factor of up to 400, with most Hg in these trenches being derived from the surface ocean. Furthermore, vertical profiles of Hg concentrations in trench cores show notable increasing trends from pre-1900 [average 51 ± 14 (1σ) ng ⋅ g−1] to post-1950 (81 ± 32 ng ⋅ g−1). This increase cannot be explained by changes in the delivery rate of organic carbon alone but also need increasing Hg delivery from anthropogenic sources. This evidence, along with recent findings on the high abundance of methylmercury in hadal biota [R. Sun et al., Nat. Commun. 11, 3389 (2020); J. D. Blum et al., Proc. Natl. Acad. Sci. U. S. A. 117, 29292–29298 (2020)], leads us to propose that hadal trenches are a large marine sink for Hg and may play an important role in the regulation of the global biogeochemical cycle of Hg.

Validation of terrestrial biogeochemistry in CMIP6 Earth system models: a review

The vital role of terrestrial biogeochemical cycles in influencing global climate change is explored by modelling groups internationally through land surface models (LSMs) coupled to atmospheric and oceanic components within Earth system models (ESMs). The sixth phase of the Coupled Model Intercomparison Project (CMIP6) provided an opportunity to compare ESM output by providing common forcings and experimental protocols. Despite these common experimental protocols, a variety of terrestrial biogeochemical cycle validation approaches were adopted by CMIP6 participants, leading to ambiguous model performance assessment and uncertainty attribution across ESMs. In this review we summarize current methods of terrestrial biogeochemical cycle validation utilized by CMIP6 participants and concurrent community model comparison studies. We focus on variables including the dimensions of evaluations, observation-based reference datasets, and metrics of model performance. To ensure objective and thorough validations for the seventh phase of CMIP (CMIP7), we recommend the use of a standard validation protocol employing a broad suite of certainty-weighted observation-based reference datasets, targeted model performance metrics, and comparisons across a range of spatiotemporal scales.

Occurrence of structural aluminum (Al) in marine diatom biological silica: Visible evidence from microscopic analysis

The global marine biogeochemical cycle of aluminum (Al) is believed to be driven by marine diatoms, due to the uptake of dissolved Al (DAl) by living diatoms from surface seawater. The occurrence of Al in diatom biogenic silica (BSi) can inhibit the dissolution of BSi, thus benefiting the effects of the ballast role of diatoms in the biological pump and forming a coupled Si-Al biogeochemical cycle. However, the occurrence mechanism of Al in marine diatoms is still unclear. In particular, whether or not Al is incorporated into the structure of BSi of living diatoms is unrevealed, resulting in difficulties in understanding the biogeochemical behaviors of Al. In this study, Thalassiosira weissflogii, a widely distributed marine diatom in marginal seas, was selected as the model to evaluate the occurrence of structural Al in BSi based on culturing experiments with the addition of DAl. The structural Al in BSi was detected by combining focused ion beam (FIB) scanning electron microscopy and energy dispersive X-ray spectroscopy (EDS) mapping analysis. Direct evidence of structural Al in living BSi was obtained for the first time. The distribution and content of this Al were revealed by the EDS-mapping analysis. The structural Al in the BSi exhibited a homogeneous distribution, and the average Al / Si atomic ratio obtained through the FIB-EDS mapping analysis was 0.011. The effects of structural Al on BSi dissolution-inhibition are discussed based on the content of this Al. The fundamental results indicate the significant contribution of marine diatoms to the biogeochemical migration of marine Al.

A Single Bacterium Capable of Oxidation and Reduction of Iron at Circumneutral pH

The biogeochemical cycle of iron (Fe) via reactions of oxidation, reduction, precipitation, and dissolution is involved in the cycle of other ecologically relevant elements, such as C, N, P, S, As, Co, Ni, and Pb. The Fe cycle on the Earth’s surface is driven by a variety of Fe(II)-oxidizing microorganisms and Fe(III)-reducing microorganisms.