Fungal Community Assembly in the Amazonian Dark Earth

Structure and impact of root-associated fungi in treatment wetland mesocosms

Root fungal endophytes have been shown to play a positive role in soil phytoremediation by immobilizing or degrading contaminants. In comparison, little is known about their ecological functions and possible role in improving plant performance in treatment wetlands. In a greenhouse study, we compared the structure of fungal communities associated with Phragmites australis roots in treatment wetland mesocosms fed with pre-treated wastewater to mesocosms fed with drinking water. We evaluated the role of water source as an environmental filter structuring fungal communities, and correlated the relative abundances of fungal taxa with key services delivered by the wetlands (i.e., biomass production and nutrient removal). Mesocosms fed with wastewater had higher fungal alpha-diversity. Contrary to expectations, many fungi were unique to drinking water-fed mesocosms, suggesting that the oligotrophic conditions prevailing in these mesocosms benefited specific fungal taxa. On the other hand, wastewater-fed mesocosms had a slightly higher proportion of sequence reads belonging to fungal species recognized as potential endophytes and phytopathogens, highlighting the potential role of wastewater as a source of plant-associated fungi. Interestingly, we found contrasted association patterns between fungal species' relative abundances and different treatment wetland services (e.g., N vs P removal), such that some fungi were positively associated with N removal but negatively associated with P removal. This suggests that fungal endophytes may be functionally complementary in their contribution to distinct mesocosm services, thus supporting arguments in favor of microbial diversity in phytotechnologies. Because of the wide alpha-diversity of fungal communities, and the fact that with current databases, most species remained unassigned to a specific function (or even guild), further investigation is needed to link fungal community structure and service delivery in treatment wetlands.

The addition of biochar and nitrogen alters the microbial community and their cooccurrence network by affecting soil properties

Biochar plays an important role in reducing the harmful environmental effects of inorganic nitrogen (N) fertilizers on agroecosystems, but the the impact mechanisms of biochar combined with N fertilizers on soil microorganisms are not clear enough. In this study, high-throughput sequencing was used to study the influences of three N fertilizer levels (0 (N0), 90 (N90) and 120 (N120) kg ha^-1) and two biochar levels (0 (B0) and 20 (B20) t ha^-1) on the soil microbial community and symbiotic network among microbial taxa in wheat fields. Compared to the control (B0N0), N fertilizer alone or combined with biochar significantly increased soil total N, available N, and organic matter in topsoil (0-20 cm), and the same results were found only in B20N120 treatment in subsoil (20-40 cm). In addition, bacterial and fungal diversity in topsoil were significantly increased and decreased by all N and biochar treatments, respectively. Moreover, soil bacterial and fungal community compositions also were also changed by N and biochar. Furthermore, biochar weakened the competition and cooperation among microorganisms in topsoil and subsoil, and the keystone species of networks were also changed by biochar. Redundancy analysis showed that soil total N, available N, available P, available K and pH were the main environmental factors driving the changes in bacterial and fungal community structures. These data indicated that the addition of N fertilizer and biochar could improve soil fertility by maintaining the stability of microbial community structures, which can provide reasonable guidance for the sustainable development of agriculture, such as maintaining dryland production.

Characteristics of carbon, nitrogen, phosphorus and sulfur cycling genes, microbial community metabolism and key influencing factors during composting process supplemented with biochar and biogas residue

Carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling functional genes and bacterial and fungal communities during composting with biochar and biogas residue amendments were studied. Correlations between microbial community structure, functional genes and physicochemical properties were investigated by network analysis and redundancy analysis. It was shown that the gene of acsA abundance accounted for about 50% of the C-related genes. Biogas residue significantly decreased the abundance of denitrification gene nirK. Biogas residues can better promote the diversity of bacteria and fungi during composting. Biochar significantly increased the abundance of Humicola. Redundancy analysis indicated that pile temperature, pH, EC were the main physicochemical factors affecting the microbial community. WSC and NO₃^--N have significant correlation with C, N, P, S functional genes. The research provides a theoretical basis for clarifying the metabolic characteristics of microbial communities during composting and for the application of biochar and biogas residues in composting.

Field-applied biochar-based MgO and sepiolite composites possess CO2 capture potential and alter organic C mineralization and C-cycling bacterial structure in fertilized soils

Agricultural soils contribute a significant amount of anthropogenic CO₂ emission, a greenhouse gas of global environmental concern. Hence, discovering sustainable materials that can capture CO₂ in cultivated soils is paramount. Since the effect of biochar on C mineralization/retention in fertilized soils is unclear, we produced biochar-based MgO and sepiolite-nanocomposites with CO₂ capture potential. The field-scale impacts of the modified-biochars were evaluated on net C exchange rate (NCER) periodically for 3 months in fertilized plots. The effects of the modified-biochar on organic-C mineralization, the activities, and dynamics of C-cycling-related 16S rRNA which are unknown, were investigated. Results revealed an initial rapid and higher cumulative CO₂ emission from the sole fertilizer treatment (F). Unlike the biochar treatment (BF), the successful incorporation of MgO/Mg(OH)₂ nanoparticles into the matrix and surface of biochar, and the potential formation of MgCO₃ with soil CO₂, mitigated CO₂ emission, especially in the MgO-modified biochar (MgOBF), compared to the sepiolite-biochar treatment (SBF). Compared to F and BF, the higher C retention as MgCO₃ in the modified biochar treatments led to an increase in cellulase activity, stimulation of key C-cycling-related bacteria, and the expression of genes associated with starch, sucrose, amino sugar, nucleotide sugar, ascorbate, aldarate, cellulose, and chitin degradation, thus, increasing organic C mineralization. Among the modified-biochar treatments, higher C mineralization was recorded in SBF, resulting in increased cumulative CO₂ emission, despite its initial capture for up to 42 days. However, MgOBF was effective in capturing soil-derived CO₂, despite the increased C mineralization compared to biochar. The changes in soil moisture and temperature significantly regulated NCER. Also, the modified biochars positively influenced the distribution of C-cycling-related bacteria by improving soil pH and available nutrients. Among the modified biochars, the observed higher mitigation effect of MgOBF on NCER indicated that it could be preferably applied in agricultural soils.

Impact of Different Biochars on Microbial Community Structure in the Rhizospheric Soil of Rice Grown in Albic Soil

The purpose of this study was to clarify the effects of biochar on the diversity of bacteria and fungi in the rice root zone and to reveal the changes in soil microbial community structure in the root zone after biochar application to provide a scientific basis for the improvement of albic soil. Rice and corn stalk biochar were mixed with albic soil in a pot experiment. Soil samples were collected at the rice maturity stage, soil nutrients were determined, and genomic DNA was extracted. The library was established using polymerase chain reaction (PCR) amplification. The abundance, diversity index, and community structure of the soil bacterial 16SrRNA gene V3 + V4 region and the fungal internal transcribed spacer-1 (ITS1) region were analyzed using Illumina second-generation high-throughput sequencing technology on the MiSeq platform with related bioinformatics. The results revealed that the biochar increased the soil nutrient content of albic soil. The bacteria ACE indexes of treatments of rice straw biochar (SD) and corn straw biochar (SY) were increased by 3.10% and 2.06%, respectively, and the fungi ACE and Chao indices of SD were increased by 7.86% and 14.16%, respectively, compared to conventional control treatment with no biochar (SBCK). The numbers of bacterial and fungal operational taxonomic units (OUT) in SD and SY were increased, respectively, compared to that of SBCK. The relationship between soil bacteria and fungi in the biochar-treated groups was stronger than that in the SBCK. The bacterial and fungal populations were correlated with soil nutrients, which suggested that the impacts of biochar on the soil bacteria and fungi community were indirectly driven by alternation of soil nutrient characteristics. The addition of two types of biochar altered the soil microbial community structure and the effect of rice straw biochar treatment on SD was more pronounced. This study aimed to provide a reference and basic understanding for albic soil improvement by biochar, with good application prospects.

Biochar-fertilizer interaction modifies N-sorption, enzyme activities and microbial functional abundance regulating nitrogen retention in rhizosphere soil

The impact of the excessive use of N fertilizer remains an environmental problem of global concern. The effect of biochar on soil N retention is still unclear, and knowledge on how a mixture of biochar and fertilizer (B-F) influence N-sorption, N-cycling enzymes activities, diversity and functional abundance of organisms regulating N-retention in rhizosphere soil is poorly understood. Therefore, biochars derived from bamboo, rice straw, cow and pig manure were characterized, and their interactions with NPK fertilizer were evaluated. Results showed that while the effect of biochar on N retention varied among biochar types, such variations increased after B-F. Unlike NH₄⁺ retention, NO₃^- retention by biochar in fertilized soil was poor (<8 weeks), but were however increased after longer periods (15 weeks) in B-F due to plant uptake, sorption and stimulation of N-cycling enzymes activities. This stimulation proved that N-fertilizer provided substrates for N-cycling organisms which was confirmed by the dominance of Proteobacteria, Chloroflexi, Actinobacteria, and Gemmatimonadetes which are important in soil N-cycling, despite the reductions in total diversity, class, phyla and genera abundance of bacterial 16SrRNA genes by B-F. This suggested that B-F induced specific organisms involved in N-cycling, which out-competed other organisms not involved in N-cycling. The provision of substrates by N-fertilizer in B-F for bacterial groups involved in N-cycling modified the rhizosphere microbial structure. The abundance of N-cycling organisms was regulated by the persistence among dominant groups, soil pH, total N, and microbial colonization induced by different biochars interacting with fertilizer which led to enhanced N-retention.

Regular Biochar and Bacteria-Inoculated Biochar Alter the Composition of the Microbial Community in the Soil of a Chinese Fir Plantation

Biochar is a promising material for the improvement of soil quality. However, studies on biochar have mostly been carried out in laboratory conditions or have focused on agricultural aspects. The impacts of the application of biochar on soil characteristics and related ecological processes of the forest ecosystem have not been fully resolved. In this study, we investigated the effects of regular biochar and bacteria-loaded biochar on the microbial communities in the bulk soil and the rhizosphere soil of an annual Chinese fir plantation. In early spring (April), the two types of biochar were added to the soil at the rates of 2.22 t·ha−1, 4.44 t·ha−1, 6.67 t·ha−1, 8.89 t·ha−1, and 11.11 t·ha−1 by ring furrow application around the seedlings, and soil samples were collected at the end of autumn (November). The results showed that biochar addition increased the soil nutrient content and promoted the growth and diversity of soil microbial communities. The diversity of soil fungi was significantly increased, and the diversity of soil bacteria was significantly decreased. Principal component analysis under the different biochar types and application rates demonstrated that microbial communities differed significantly between the treatments and controls and that the effect of biochar on the microbial community of the bulk soil was more significant than that of the rhizosphere soil. Under the same dosage, the effect of bacteria-loaded biochar on soil was more significant than that of regular biochar.

Crop types have stronger effects on soil microbial communities and functionalities than biochar or fertilizer during two cycles of legume-cereal rotations of dry land

The addition of biochar to agricultural fields has been widely studied, but most of these studies have emphasized its effects by growing a single type of crop over short- to long-term time spans. Additionally, a limited number of studies have focused on the soil microbial community composition with respect to biochar addition in legume-cereal crop rotation. In this study, we examined soil microbial community structures by adding biochar (0, 5, and 10 t ha^-1) and fertilizer (nitrogen-N, phosphorous-P and potassium-K) during 2 cycles of mash bean and wheat rotations. The results showed that the bacterial (16S rRNA) gene abundance was often increased by biochar addition in the presence of mash bean (Vigna mungo L.) but not wheat. When the soil received fertilizer, the bacterial gene abundance was less responsive to biochar addition. Fungal (ITS rRNA) copy numbers were enhanced by biochar and fertilizer in presence of wheat but were decreased in the presence of mash bean. Fertilizer addition also resulted in less change in ITS genes after biochar addition. Microbial functional groups including Gram⁺, Gram^- and Pseudomonas bacteria were stimulated by biochar or fertilizer only in mash bean soils, while mycorrhizae were significantly increased by biochar in wheat soils. Although biochar addition affected soil properties, microbial community assays were not greatly altered by these physicochemical properties. In conclusion, the crop type played a decisive role, rather than biochar or fertilizer addition, in shaping microbial community structures (16S and ITS phyla) during crop rotation.

Response of fungal communities in different soils to biochar and chemical fertilizers under simulated rainfall conditions

Biochar is a good soil additive, which cannot only effectively store carbon, but also improve soil fertility and crop yield. However, the specific response of fungal communities to biochar and chemical fertilizers are still relatively lacking. In addition, most studies do not take into account rainfall factors when conducting culture experiments. In the case of simulated rainfall, we investigated the response of fungal communities in different soils to biochar and fertilizers in China and analyzed the correlation between chemical properties and different fungal species. The tested soils were yellow-brown soil, fluvo-aquic soil, lou soil and black soil, and the simulated daily rainfall was 25 mm. The results indicated that the application of biochar and chemical fertilizers had a greater impact on the alpha diversity of acidic soils (yellow-brown soil, fluvo-aquic soil), but less on alkaline soils (lou soil, black soil). The relative abundance of Ascomycetes was most affected by biochar and fertilizer in any soil. From the point of view of the fungal community, yellow-brown soil was more suitable for single application of biochar, because it not only improved the ability of the soil to degrade persistent organic matter but also inhibited the spread of soil pathogens. In black soil, the relative abundance of Fusarium was significantly reduced by the combined application of biochar and chemical fertilizers (FC), and the decline was much higher than several other bacteria. However, FC caused the greatest changes in the structure of all soil fungal communities. Moreover, there was a significant correlation between the content of available nutrients and composition of fungal community in fluvo-aquic soil. In summary, it can be explained that the effects of biochar and chemical fertilizers on soil fungi may vary depending on the soil type, so it is very urgent to conduct long-term research on different typical soils.

Effects of biochar amendment on bacterial and fungal communities in the reclaimed soil from a mining subsidence area

Biochar amendment of soil is well known to improve soil fertility and microbial function. However, little is known about the effect of biochar addition to reclaimed soil in coal mining subsidence area on microbial community. A plant soil cultivation experiment was conducted with wheat grown and four treatments were included: P and K fertilizer (CK); NPK inorganic fertilizer (NPK); NPK inorganic fertilizer and straw (NPKS); and NPK inorganic fertilizer and biochar (NPKB). The results indicated that biochar amendment significantly increased the concentrations of NH₄⁺-N, total N, and available P and K compared with the NPK. Biochar addition also significantly increased the grain yield and total biomass of wheat. Furthermore, biochar amendment treatment increased the absolute abundance and altered the community structure of soil bacteria and fungi in the reclaimed soil. Illumina MiSeq sequencing showed that the addition of biochar increased α-diversity of bacteria and relative abundances of Proteobacteria, Actinobacteria, and Bacteroidetes, whereas the relative abundance of Firmicutes were decreased by 61%. However, biochar addition did not change the relative abundance of dominant fungal phyla. Redundancy analysis (RDA) suggested that total N, available P, and K contents were the key factors correlated with changes in microbial community structure. Overall, our results suggest that biochar amendment in reclaimed soil in coal mine subsidence area could increase wheat yield and abundance and alter microbial community compositions.

Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths

The socio-economic values of fertile and carbon-rich Dark Earth soils are well described from the Amazon region. Very recently, Dark Earth soils were also identified in tropical West Africa, with comparable beneficial soil properties and plant growth-promoting effects. The impact of this management technique on soil microbial communities, however, is less well understood, especially with respect to the ecologically relevant group of arbuscular mycorrhizal (AM) fungi. Thus, we tested the hypotheses that (1) improved soil quality in African Dark Earth (AfDE) will increase soil microbial biomass and shift community composition and (2) concurrently increased nutrient availability will negatively affect AM fungal communities. Microbial communities were distinct in AfDE in comparison to adjacent sites, with an increased fungal:bacterial ratio of 71%, a pattern mainly related to shifts in pH. AM fungal abundance and diversity, however, did not differ despite clearly increased soil fertility in AfDE, with 3.7 and 1.7 times greater extractable P and total N content, respectively. The absence of detrimental effects on AM fungi, often seen following applications of inorganic fertilizers, and the enhanced role of saprobic fungi relevant for mineralization and C sequestration support previous assertions of this management type as a sustainable alternative agricultural practice.