Biology subjects

Tsai, S. M.

Publications and source records attributed to Tsai, S. M..

8 recordsLinked to original sources

bioRxiv2025

Connectivity of restored Atlantic Forest fragments drives composition and functionality of the fungal community in the leaf litter layer

The restoration of biodiversity and functional tropical forests is critical to mitigating global biodiversity losses. Aboveground, increasing the connectivity of regenerating forests fragments facilitates the recolonization of tropical forest biodiversity. However, restoring functional ecosystems also requires the recovery of decomposition processes as these are essential in shaping aboveground biodiversity. Therefore, we investigate the role of forest connectivity on restoring the composition and functioning of fungal communities in the leaf litter layer during a chronosequence of forest restoration. In the Brazilian Atlantic Forest, we studied secondary forests regrown between 18 to 55 years after deforestation and different levels of forest connectivity and compared their litter to recently abandoned pastures and undisturbed primary forests. We quantified how forest age and connectivity between fragments influenced the litter fungi composition in relation to tree diversity, litter chemistry, and litter isotopes. We show that fungal composition was highly heterogeneous in forest litter, whereas pasture litter exhibited a more homogeneous community. Moreover, forest connectivity had stronger effects on litter fungal composition compared to forest age. Connectivity promoted wood saprotrophs and endophytes, while suppressed soil saprotrophs, with its effects being more evident during later stages of restoration. Fungal guilds such as endophytes and saprophytes, were primarily influenced by tree diversity and leaf litter chemistry. We conclude that forest connectivity promotes the re-establishment of saprophytic fungi capable of decomposing recalcitrant litter substrates, driven mainly by enhancing tree diversity and litter quality. Practical implications of increasing connectivity may relate to forest resilience on front of future climate change scenarios.

microbiology↗

bioRxiv2025

Microbial and organic matter composition jointly drive phosphorus cycling genes and phosphorus availability in Amazonian soils

Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. However, forest-to-agriculture conversion changes plant-microbe-soil interactions, affecting P cycling, which may additionally changed by land-use intensity. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus plantation. We investigated how microbial and water-extractable organic matter (WEOM) composition interacted with soil physicochemical attributes and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and WEOM composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus plantation. Proteobacteria and nutrient-rich WEOM were more abundant in the agroforest, whereas Ascomycota and nutrient-poor WEOM predominated the citrus plantation. Genes related to "P acquisition" were more abundant in agroforest soils, while genes related to "P-compound synthesis" were more abundant in citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and WEOM resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.

microbiology↗

bioRxiv2024

Liming pasture soils in the Amazon region promotes low-affinity methane oxidation by type I and II methanotrophs

In the Amazon Forest region, cattle pastures are the main land use subsequent to deforestation. This land-use change affects the soil microbial community and methane fluxes, shifting the soil from a methane sink to a source. Soil physical and chemical attributes are changed due to slash-and-burn processes, including an increased soil pH after forest-to-pasture conversion. Without amendments, the pasture soils can become acidic again resulting in many cases in soil degradation. Liming is a standard management practice to increase soil pH while decreasing Al3+ availability. Liming is important to recover these degraded lands and increase soil fertility, but its impact on soil methane cycling in tropical soils is unknown. Here we investigated the role of soil pH on methane uptake under high concentrations of the gas. The top layer of forest (pH 4.1) and adjacent pasture soils (pH 4.8) from the Eastern Amazon were subjected to liming treatment (final pH 5.8) and incubated with [~]10,000 ppm of 13CH4 for 24 days to label DNA with 13C. Soil DNA was evaluated with Stable Isotopic Probing (SIP-DNA), methanotrophic abundance was quantified (pmoA gene), and high throughput sequencing of 16S rRNA was performed. Liming increased the methane uptake in both forest ([~]10%) and pasture ([~]25%) soils. Methanotrophs Methylocaldum sp. (type I) and Beijerinckaceae (type II) were identified to actively incorporate carbon from methane in limed pasture soils. In limed forest soils, Nitrososphaeraceae, Lysobacter sp., and Acidothermus sp. were identified as 13C-enriched taxa. The enrichment of the archaeal family Nitrososphaeraceae, known as ammonia oxidizers, is correlated with an increase of ammonia monooxygenase genes, which code for an enzyme complex with wide substrate specificity that can also perform methane oxidation. In conclusion, liming Amazonian pasture soils not only contributes to the fertility and recovery of degraded areas but also has the potential to improve the oxidation of methane at high concentrations of this gas.

ecology↗

bioRxiv2022

Dynamics of methane cycling microbiome during methane flux hot moments from riparian buffer systems

Riparian buffer systems (RBS) are a common agroforestry practice that consists of keeping a forested boundary adjacent to water bodies in agricultural landscapes, thus helping to protect aquatic ecosystems from adverse impacts. Nevertheless, despite the multiple benefits they provide, RBSs can be hotspots of methane emissions since abundant organic carbon and high-water tables are often found in these soils. In southern Ontario, Canada, the rehabilitation of Washington Creeks streambank occurred in 1985. In a recent study, methane (CH4) fluxes were measured biweekly for two years (2017-2018) in four different vegetative riparian areas alongside Washington creek: a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR) for comparison. Based on methane fluxes in 2018 and hot moments identified, we selected two dates from summer (July 04 and August 15) and use soil sampling from those days to assess the CH4 cycling microbial communities in these RBS. We used qPCR and high-throughput sequencing from both DNA and cDNA to measure the diversity and activity of the methanogen and methanotroph communities. Methanogens were abundant in all riparian soils, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus Methanoreggula, but they were mostly active in UNF soils. Among methanotrophs, Methylocystis was the most abundant taxon in all the riparian sites, except for AGR soils where the methanotrophs community mostly comprised members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USC). In summary, these results indicate that differences in CH4 fluxes between RBS at Washington creek are influenced by differences in the presence and activity of methanogens, which were higher in the deciduous forest (UNF) soils during hot moments CH4 flux, likely due to high water content in that soils. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/517857v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1dcde21org.highwire.dtl.DTLVardef@17b59e5org.highwire.dtl.DTLVardef@14adfb0org.highwire.dtl.DTLVardef@a3b411_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Maintaining grass coverage increases methane uptake in Amazonian pasture soils

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest- to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. In parallel, we assessed changes in the soil microbial community structure of both bare pasture soil as well as rhizosphere soil through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that liming compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, if compared to a bare pasture soil.

microbiology↗

bioRxiv2020

Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here we provide the first report of the in situ seasonal dynamics of CH4 cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH4 cycling microbial communities and further investigated their responses to seasonal changes. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the methanogenic (methyl coenzyme-M reductase - mcrA) and methanotrophic (particulate methane monooxygenase - pmoA) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry, but also the composition of the microbial communities. The results presented may contribute to the understanding of the current state of CH4 cycling in this region.

microbiology↗

bioRxiv2020

Belowground changes to community structure alter methane-cycling dynamics in Amazonia

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with changes to ecosystem processes, including substantial increases in soil methane (CH4) emission. The drivers of this change in CH4 flux are not well understood. To address this knowledge gap, we measured soil CH4 flux, environmental conditions, and belowground microbial community attributes across a land use change gradient (old growth primary forest, cattle pasture, and secondary forest regrowth) in two Amazon Basin regions. Primary forest soils exhibited CH4 uptake at modest rates, while pasture soils exhibited CH4 emission at high but variable rates. Secondary forest soils exhibited low rates of CH4 uptake, suggesting that forest regrowth following pasture abandonment could reverse the CH4 sink-to-source trend. While few environmental variables were significantly associated with CH4 flux, we identified numerous microbial community attributes in the surface soil that explained substantial variation in CH4 flux with land use change. Among the strongest predictors were the relative abundance and diversity of methanogens, which both increased in pasture relative to forests. We further identified individual taxa that were associated with CH4 fluxes and which collectively explained ~50% of flux variance. These taxa included methanogens and methanotrophs, as well as taxa that may indirectly influence CH4 flux through acetate production, iron reduction, and nitrogen transformations. Each land type had a unique subset of taxa associated with CH4 fluxes, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, our results suggest that changes in CH4 flux from agricultural conversion could be driven by microbial responses to land use change in the surface soil, with both direct and indirect effects on CH4 cycling. This demonstrates the central role of microorganisms in mediating ecosystem responses to land use change in the Amazon Basin.

ecology↗

bioRxiv2020

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink that is threatened by agricultural conversion. Rainforest-to-pasture conversion leads to the release of a potent greenhouse gas by converting soil from a methane sink into a source. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarem, Para and Ariquemes, Rondonia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could explain the greater methane flux. Furthermore, we found that secondary rainforests recovered as methane sinks, indicating the potential for reforestation to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

microbiology↗