Understanding changes in biocrust communities following phosphate mining in the Negev Desert

Isolation of biocrust cyanobacteria and evaluation of Cu, Pb, and Zn immobilisation potential for soil restoration and sustainable agriculture

Soil contamination by heavy metals represents an important environmental and public health problem of global concern. Biocrust-forming cyanobacteria offer promise for heavy metal immobilisation in contaminated soils due to their unique characteristics, including their ability to grow in contaminated soils and produce exopolysaccharides (EPS). However, limited research has analysed the representativeness of cyanobacteria in metal-contaminated soils. Additionally, there is a lack of studies examining how cyanobacteria adaptation to specific environments can impact their metal-binding capacity. To address this research gap, we conducted a study analysing the bacterial communities of cyanobacteria-dominated biocrusts in a contaminated area from South Sardinia (Italy). Additionally, by using two distinct approaches, we isolated three Nostoc commune strains from cyanobacteria-dominated biocrust and we also evaluated their potential to immobilise heavy metals. The first isolation method involved acclimatizing biocrust samples in liquid medium while, in the second method, biocrust samples were directly seeded onto agar plates. The microbial community analysis revealed Cyanobacteria, Bacteroidota, Proteobacteria, and Actinobacteria as the predominant groups, with cyanobacteria representing between 13.3 % and 26.0 % of the total community. Despite belonging to the same species, these strains exhibited different growth rates (1.1-2.2 g L-1 of biomass) and capacities for EPS production (400-1786 mg L-1). The three strains demonstrated a notable ability for metal immobilisation, removing up to 88.9 % of Cu, 86.2 % of Pb, and 45.3 % of Zn from liquid medium. Cyanobacteria EPS production showed a strong correlation with the removal of Cu, indicating its role in facilitating metal immobilisation. Furthermore, differences in Pb immobilisation (40-86.2 %) suggest possible environmental adaptation mechanisms of the strains. This study highlights the promising application of N. commune strains for metal immobilisation in soils, offering a potential bioremediation tool to combat the adverse effects of soil contamination and promote environmental sustainability.

Corn straw biochar addition elevated phosphorus availability in a coastal salt-affected soil under the conditions of different halophyte litter input and moisture contents

Improving salt-affected soil health using different strategies is of great significance for Sustainable Development Goals. The effects of biochar as a sustainable carbon negative soil amendment on phosphorous (P) pools in the degraded salt-affected soils of the of coastal wetlands (as one of the primary blue carbon ecosystems) with halophyte litter input under different water conditions (the two intrinsic characteristics of coastal wetlands) are poorly understood. Thus, a corn straw derived biochar (CBC) was added into a coastal salt-affected soil collected from the Yellow River Delta to investigate its effect on P fractions and availability under the input of three different local halophyte litters (i.e., Suaeda salsa, Imperata cylindrica and Phragmites australis) and under the unflooded and flooded water conditions. The results showed that the individual input of Suaeda salsa increased soil P availability by 28.2-40.9 %, but Imperata cylindrica and Phragmites australis had little effect on P availability. CBC individual amendment more efficiently enhanced P availability in the unflooded soil than the flooded soil. However, the co-amendment of CBC with litters showed little synergistic effect on P availability. CBC sharply increased the proportion of Ca-bound labile P fraction, but moderately lifted the proportion of Al/Fe-bound mediumly labile P fraction. CBC-enhanced P availability and altered inorganic P fractions were mainly resulted from the provision of labile inherent P by biochar, improved soil properties (i.e., increased CEC), and altered bacterial community composition (i.e., elevated abundance of P-solubilizing and phosphate-accumulating bacteria). These findings give new insights into understanding P biogeochemical cycling in the coastal salt-affected soils amended with biochars, and will be helpful to develop biochar-based technologies for enhancing P pools and improving soil health of the blue carbon ecosystems.

Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light

Although most cyanobacteria use visible light (VL; λ = 400-700 nm) for photosynthesis, some have evolved strategies to use far-red light (FRL; λ = 700-800 nm). These cyanobacteria are defined as far-red light-utilizing cyanobacteria (FRLCyano), including two groups: (1) chlorophyll d-producing Acaryochloris spp. and (2) polyphyletic cyanobacteria that produce chlorophylls d and f in response to FRL. Numerous ecological studies examine pigments, such as chlorophylls d and f, to investigate the presence of FRLCyano in the environment. This method is not ideal because it can only detect FRLCyano that have made chlorophylls d or f. Here we develop a new method, far-red cyanobacteria identification (FRCI), to identify FRLCyano based on 16S rRNA gene sequences. From public databases and published articles, 62 16S rRNA gene sequences of FRLCyano were extracted. Comparing with related lineages, we determined that 97% sequence identity is the optimal cut-off for distinguishing FRLCyano from other cyanobacteria. To test the method experimentally, we collected samples from 17 sites in Taipei, Taiwan, and conducted VL and FRL enrichments. Our results demonstrate that FRCI can detect FRLCyano during FRL enrichments more sensitively than pigment analysis. FRCI can also resolve the composition of FRLCyano at the genus level, which pigment analysis cannot do. In addition, we applied FRCI to published datasets and discovered putative FRLCyano in diverse environments, including soils, hot springs and deserts. Overall, our results indicate that FRCI is a sensitive and high-resolution method using 16S rRNA gene sequences to identify FRLCyano.

Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.

Biochar addition regulates soil phosphorus fractions and improves release of available phosphorus under freezing-thawing cycles

Currently, the shortage of phosphorus resources is becoming more and more serious. In general, phosphorus fertilizer is poorly utilized in soil and tends to gradually accumulate. Freezing-thawing cycles (FT) are seasonal phenomenon occurring in high latitudes and altitudes regions, which have obvious influence on the form of phosphorus in soil. This study investigates the effect of biochar on soil physicochemical properties, phosphorus form and availability under FT and thermostatic incubation (TH) condition. Compared with treatment without biochar, 4 % biochar addition increased the soil pH value, electrical conductivity, organic matter and Olsen-P of soil by a maximum of 0.76, 285.55 μS/cm, 28.60 g/kg and 139.27 mg/kg, respectively. Moreover, according to Hedley-P classification results, under FT condition, the content of labile phosphorus pool is always higher than those under TH. FT may promote the conversion of phosphorus from other fractions to labile phosphorus pool. Redundancy analysis results show that biochar addition and FT can not only directly change the soil phosphorus pool, but also alter the soil physicochemical properties and microbial community, which further affect the adsorption and mineralization of phosphorus in soil. The results of this study will be devoted to understanding the changes in soil phosphorus fractions under the effects of biochar addition and FT, providing references for agricultural production in areas where FT occur.

Human-Dominated Land Use Change in a Phosphate Mining Area and Its Impact on the Water Environment

The Peace River is a critical water source in southwest Florida, United States. The watershed contains many phosphate mines that decrease water safety. Whether phosphate mining leads to a reduction in surface runoff and affects water quality in the Peace River Basin has been a highly controversial subject. Thus, the environmental impacts of phosphate mining in the Peace River were assessed. The Soil and Water Assessment Tool (SWAT) model is a widely used physical-mechanism-based distributed hydrological model that uses spatial distribution data, such as topography, soil, land use, and weather, to predict water, sediment, nutrient, pesticide, and fecal bacteria production. Based on a SWAT model, runoff, total nitrogen (TN) load, and total phosphorus (TP) load at the outlet of the Peace River Basin from 2001 to 2018 were investigated. The applicability of the four uncertainty methods in the hydrological simulation of the basin was assessed. The runoff at five stations in a specified mining area was simulated to analyze the impact of human-dominated land use changes caused by phosphate mining on the water environment. The results for the pre- and post-mining periods showed that the land use transfer in the study area experienced large fluctuations and that the land use change had a significant impact on the runoff (the outlet site decreased by 44.14%), indicating that phosphate mining has a significant effect on reducing runoff in the basin. An analysis of three scenarios (pre-mining [s1], post-mining [s2], and reclamation [s3]) showed that during s1–s2–s3, the change in mining land area is large (increased by 142.86%) and that TN and TP loads increased, indicating that human activities mainly affect the water environment through phosphate mining. This is mainly because a large amount of wastewater containing high concentrations of inorganic chemicals, which is produced in the process of phosphate mining and processing, overflows directly or from the sedimentation tank into the river. In summary, the simulation results showed that the changes in runoff and pollutants were attributed to phosphate rock mining. Therefore, strengthening the management of phosphate mining and adopting effective protection measures is of substantial significance for the effective protection of water resources. By analyzing the measured data, this study can help people understand more actual situations and further evaluate the impact of phosphate mining activities on the water environment. The simulation results can also be used to predict the future trend of runoff and water quality in the Peace River Basin and provide a decision-making basis for government management departments to issue water resource protection measures.