Regulation Of Biogeochemical Cycles Research Articles

Evolutionary pathways for deep-sea adaptation in marine planktonic Actinobacteriota.

The deep ocean, one of the largest ecosystems on earth, is dominated by microorganisms that are keystones in the regulation of biogeochemical cycles. However, the evolutionary pathways underlying the specific adaptations required (e.g., high pressure and low temperature) by this unique niche remain understudied. Here, we analyzed the first representatives belonging to the order Acidimicrobiales, a group of marine planktonic Actinobacteriota, that specifically inhabits the aphotic zone of the oceanic water column (>200 m). Compared with their epipelagic counterparts, deep-sea representatives showed the same evolution in genome architecture with higher GC content, longer intergenic spaces as well as higher nitrogen (N-ARSC) and lower carbon (C-ARSC) content in encoded amino acid residue side chains consistent with the higher nitrogen concentration and lower carbon concentration in deep waters compared to the photic zone. Metagenomic recruitment showed distribution patterns that allowed the description of different ecogenomic units within the three deep water-associated genera defined by our phylogenomic analyses (UBA3125, S20-B6 and UBA9410). The entire genus UBA3125 was found exclusively associated with oxygen minimum zones linked to the acquisition of genes involved in denitrification. Genomospecies of genus S20-B6 recruited in samples from both mesopelagic (200-1,000 m) and bathypelagic (1000-4,000 m) zones, including polar regions. Diversity in the genus UBA9410 was higher, with genomospecies widely distributed in temperate zones, others in polar regions, and the only genomospecies associated with abyssal zones (>4,000 m). At the functional level, groups beyond the epipelagic zone have a more complex transcriptional regulation including in their genomes a unique WhiB paralog. In addition, they showed higher metabolic potential for organic carbon and carbohydrate degradation as well as the ability to accumulate glycogen as a source of carbon and energy. This could compensate for energy metabolism in the absence of rhodopsins, which is only present in genomes associated with the photic zone. The abundance in deep samples of cytochrome P450 monooxygenases associated with the genomes of this order suggests an important role in remineralization of recalcitrant compounds throughout the water column.

Spatial Variation of Microbial Community Structure and Its Driving Environmental Factors in Two Forest Types in Permafrost Region of Greater Xing′an Mountains

Climate warming is accelerating permafrost degradation. Soil microorganisms play key roles in the maintenance of high-latitude permafrost regions and forest ecosystems’ functioning and regulation of biogeochemical cycles. In this study, we used Illumina MiSeq high-throughput sequencing to investigate soil bacterial community composition at a primeval Larix gmelinii forest and a secondary Betula platyphylla forest in a permafrost region of the Greater Xing’an Mountains. The Shannon diversity index tended to decrease and then increase with increasing soil depth, which was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 40–60 cm. Proteobacteria (19.86–29.68%), Acidobacteria (13.59–31.44%), Chloroflexi (11.04–27.19%), Actinobacteria (7.05–25.57%), Gemmatimonadetes (1.76–9.18%), and Verrucomicrobia (2.03–7.00%) were the predominant phyla of the bacterial community in two forest types. The relative abundance of Proteobacteria showed a decreasing trend in the B. platyphylla forest and an increasing trend in the L. gmelinii forest, whereas that of Chloroflexi increased and then decreased in the B. platyphylla forest and decreased in the L. gmelinii forest with increasing soil depth. The relative abundance of Acidobacteria was significantly higher in the B. platyphylla forest than in the L. gmelinii forest at 0–20 cm depth, whereas that of Actinobacteria was significantly higher in the L. gmelinii forest than in the B. platyphylla forest at 0–20 cm and 40–60 cm depth. Principal coordinate analysis (PCoA) and two-way analysis of variance (ANOVA) indicated that microbial community composition was more significantly influenced by forest type than soil depth. Redundancy analysis (RDA) showed that microbial community structure was strongly affected by soil physicochemical properties such as nitrate nitrogen (NO3−-N), pH, and total organic carbon (TOC). These results offer insights into the potential relationship between soil microbial community and forest conversion in high latitude permafrost ecosystems.

Vertical distribution of bacterial community diversity in the Greater Khingan Mountain permafrost region

Soil microorganisms are crucial contributors to the function of permafrost ecosystems, as well as the regulation of biogeochemical cycles. However, little is known about the distribution patterns and drivers of high‐latitude permafrost microbial communities subject to climate change and human activities. In this study, the vertical distribution patterns of soil bacterial communities in the Greater Khingan Mountain permafrost region were systematically analyzed via Illumina Miseq high‐throughput sequencing. Bacterial diversity in the active layer was significantly higher than in the permafrost layer. Principal coordinate analysis (PCoA) indicated that the bacterial community structure in the active layer and the permafrost layer was completely separated. Permutational multivariate analysis of variance (PERMANOVA) detected statistically significant differentiation across the different depths. The relative abundance of the dominant phyla Chloroflexi (17.92%–52.79%) and Actinobacteria (6.34%–34.52%) was significantly higher in the permafrost layer than in the active layer, whereas that of Acidobacteria (4.98%–38.82%) exhibited the opposite trend, and the abundance of Proteobacteria (2.49%–22.51%) generally decreased with depth. More importantly, the abundance of bacteria linked to human infectious diseases was significantly higher in the permafrost layer according to Tax4Fun prediction analysis. Redundancy analysis (RDA) showed that ammonium nitrogen (NH4 +‐N), total organic carbon (TOC), and total phosphorus (TP) were major factors affecting the bacterial community composition. Collectively, our findings provide insights into the soil bacterial vertical distribution patterns and major environmental drivers in high‐latitude permafrost regions, which is key to grasping the response of cold region ecosystem processes to global climate changes.

Vertical distribution patterns and drivers of soil bacterial communities across the continuous permafrost region of northeastern China

BackgroundSoil microorganisms in the thawing permafrost play key roles in the maintenance of ecosystem function and regulation of biogeochemical cycles. However, our knowledge of patterns and drivers of permafrost microbial communities is limited in northeastern China. Therefore, we investigated the community structure of soil bacteria in the active, transition and permafrost layers based on 90 soil samples collected from 10 sites across the continuous permafrost region using high-throughput Illumina sequencing.ResultsProteobacteria (31.59%), Acidobacteria (18.63%), Bacteroidetes (9.74%), Chloroflexi (7.01%) and Actinobacteria (6.92%) were the predominant phyla of the bacterial community in all soil layers; however, the relative abundances of the dominant bacterial taxa varied with soil depth. The bacterial community alpha-diversity based on the Shannon index and the phylogenetic diversity index both decreased significantly with depth across the transition from active layer to permafrost layer. Nonmetric multidimensional scaling analysis and permutation multivariate analysis of variance revealed that microbial community structures were significantly different among layers. Redundancy analysis and Spearman’s correlation analysis showed that soil properties differed between layers such as soil nutrient content, temperature and moisture mainly drove the differentiation of bacterial communities.ConclusionsOur results revealed significant differences in bacterial composition and diversity among soil layers. Our findings suggest that the heterogeneous environmental conditions between the three soil horizons had strong influences on microbial niche differentiation and further explained the variability of soil bacterial community structures. This effort to profile the vertical distribution of bacterial communities may enable better evaluations of changes in microbial dynamics in response to permafrost thaw, which would be beneficial to ecological conservation of permafrost ecosystems.

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan.

Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

Influence of vegetation type on the ecosystem services provided by urban green areas in an arid zone of northern Mexico

Urban green areas (UGA) in arid regions potentially offer ecosystem services such as the regulation of biogeochemical cycles (water and carbon), which can help make efficient use of water and mitigate climate change in these areas. However, the type of vegetation (native or exotic) in a given area can directly influence the ability of UGAs to provide these services. Arid zones are characterized by water scarcity, so making efficient use of water in UGAs is relevant, especially in a climate change scenario. In order to understand the influence of xerophilous native and exotic vegetation on the hydrological and carbon cycles of UGAs in arid zones, we used two approaches: field observations in UGAs and greenhouse experimentation to simulate drought in mesocosms with the native and exotic vegetation of arid zones. We determine plant water use to maintain the aesthetical appearance (amount of irrigation, evapotranspiration rate, and water efficiency), for climate regulation influence, measure the carbon released to the atmosphere (soil respiration: RS), and the soil carbon storage as an indicator of support service. The results show that in arid zones, the UGAs with xerophilous native vegetation use water more efficiently and their soil carbon release is lower, even in periods of drought, mainly due to their adaptation to climate conditions. The results of this study can be used by decision-makers who should encourage the use of native species in the UGAs in arid zones since they offer more environmental services than exotic species do.

Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review.

Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.

The soil fungal community of native woodland in Andean Patagonian forest: A case study considering experimental forest management and seasonal effects

Forest management can alter soil fungal communities which are important in the regulation of biogeochemical cycles and other ecosystem services. The current challenge of sustainable management is that management be carried out while preserving the bioecological aspects of ecosystems. Mixed Patagonian woodlands are subject to continuous disturbance (fire, wood extraction, and livestock), with unknown consequences for soil fungal communities. Our objective was to study the fungal community and the effects of an experimental forest management program, which combines harvesting and implantation, on the soil fungal communities in Patagonian woodland, in Argentina; considering contrasting seasons and soil parameters. At site level, the mixed woodlands appear to have greater soil cover with AM plants and soil chemical characteristics similar to other forest environments in the same region, with an intermediate fungal diversity value. When the seasonal effect was analyzed, no changes were observed in the fungal richness and diversity index, whereas modifications were recorded in the class level, in the ecological guilds, and in certain soil parameters; the inversion of phyla should be highlighted. Ascomycota and Basidiomycota were the predominant phyla, and presented a tendency to an inversion between seasons: Ascomycota fungi predominated in autumn, while Basidiomycota were more abundant in summer. The Glomeromycota were not well represented in this study. The most abundant classes were Agaricomycetes, followed by Leotiomycetes, Sordariomycetes, and Tremellomycetes, with some changes in the proportions between the two seasons, which could be related to certain soil characteristics. The most abundant orders in both seasons were Agaricales, Helotiales, Mortierellales, and Filobasidiales, correlated with some soil characteristics. The ordination analysis (NMDS) showed a correlation between taxonomic assignation and some soil characteristics, and only between class seasons. The most abundant ecological guild was saprotrophs (in both seasons: Hygrocybe, Mortierella, Cryptococcus), followed by plant pathogens (Ilyonectria, which increase in autumn); and the ectomycorrhizal symbiont (Hygrocybe in both seasons, while in summer Cortinarius, Clitopilus, and Geoglossum), all are related to C and N cycle. The only post-management changes observed in soil fungal community and chemical characteristics were in fungal richness (OTUs) and available phosphorus values; all the others (diversity indexes, taxonomy, and ecological guilds) were unaffected by this anthropic disturbance. It should be highlighted that available P and fungal species richness could be proposed as bioindicators. Future studies in native management programs, considering other aspects such as diversity of vegetation uses and system functions of the area will allow us to assess whether some of these changes are early bio-indicators of sustainable use and management.

Management of Soil Resources for Sustainable Development under a Changing Climate

Development was conventionally driven by one particular need, without fully considering the wider or future impacts. This kind of approach has now been considered to be responsible for the economic and environmental catastrophes that humans are facing: from large scale financial crises caused by irresponsible banking to the changes in global climate resulting from our dependence on fossil fuel based energy sources. Soils provide essential ecosystem services such as primary production, regulation of biogeochemical cycles (with consequences for the climate), water filtration, resistance to diseases and pests, and regulation of above-ground biodiversity. Changing of the climate systems is unequivocal. Adaptation to global climate change through improved soil quality by adoption of improved management practices is key to maintaining sustainable agricultural production. A holistic approach to soil management as the engine for increasing productivity by increasing resource use efficiency and making agriculture environmentally compatible is more important than ever before. Strategies of greenhouse gas emission reduction include those that increase the use efficiency of inputs. Herein, we discussed how management and protection of soil resources can contribute to sustainable development through sustainable agricultural production while maintaining sustenance of soil fertility.
 J. Environ. Sci. & Natural Resources, 11(1-2): 159-170 2018

Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils

BackgroundClimate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season.ResultsThe analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted.ConclusionsWe demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.

Integrated crop–livestock systems: Strategies to achieve synergy between agricultural production and environmental quality

A need to increase agricultural production across the world for food security appears to be at odds with the urgency to reduce agriculture's negative environmental impacts. We suggest that a cause of this dichotomy is loss of diversity within agricultural systems at field, farm and landscape scales. To increase diversity, local integration of cropping with livestock systems is suggested, which would allow (i) better regulation of biogeochemical cycles and decreased environmental fluxes to the atmosphere and hydrosphere through spatial and temporal interactions among different land-use systems; (ii) a more diversified and structured landscape mosaic that would favor diverse habitats and trophic networks; and (iii) greater flexibility of the whole system to cope with potential socio-economic and climate change induced hazards and crises. The fundamental role of grasslands on the reduction of environmental fluxes to the atmosphere and hydrosphere operates through the coupling of C and N cycles within vegetation, soil organic matter and soil microbial biomass. Therefore, close association of grassland systems with cropping systems should help mitigate negative environmental impacts resulting from intensification of cropping systems and improve the quality of grasslands through periodic renovations. However, much research is needed on designing appropriate spatial and temporal interactions between these systems using contemporary technologies to achieve the greatest benefits in different agro-ecological regions. We postulate that development of modern integrated crop–livestock systems to increase food production at farm and regional levels could be achieved, while improving many ecosystem services. Integrated crop–livestock systems, therefore, could be a key form of ecological intensification needed for achieving future food security and environmental sustainability.

Grand Challenges in Terrestrial Microbiology

Grand Challenges in Terrestrial Microbiology