Asymbiotic nitrogen fixation in the phyllosphere of the Amazon forest: Changing nitrogen cycle paradigms

Asymbiotic Nitrogen Fixation in the Phyllosphere of Urban Green Spaces

Biological nitrogen fixation (BNF) is an important source of nitrogen in ecosystems. Compared to symbiotic nitrogen-fixing microorganisms, free-living diazotrophic bacteria have a broader distribution and greater diversity, demonstrating greater potential for application. Leaf surfaces constitute one of the largest microbial reservoirs on Earth, harboring a variety of free-living diazotrophic bacteria, contributing significantly to plant N acquisition and growth. The distribution patterns, abundance, diversity, and the environmental variables affecting the asymbiotic nitrogen fixation (ANF) rates of free-living diazotrophic bacteria of non-leguminous plants in urban green spaces were investigated using high-throughput sequencing of nifH gene amplicons and the acetylene reduction method. Both green space type and plant species significantly impact ANF rates and nifH gene abundance in the phyllosphere, with green space type having a more pronounced effect. Leaf metal elements iron (Fe), molybdenum (Mo), and the free-living diazotrophic bacteria of the genus Skermanella collectively influence the ANF rates in the phyllosphere of urban green spaces. Linear regression analysis revealed that metal elements Fe, Mo, and potassium (K) in the leaves were significantly positive correlated with the diversity of the free-living diazotrophic bacteria and the abundance of the N-fixing gene nifH. The alpha diversity and symbiotic network structure of the free-living diazotrophic bacterial community in the phyllosphere indicated a significant negative correlation between human disturbance and environmental perturbation and the biodiversity and network complexity of these bacteria. This study provides a crucial foundation for understanding the nitrogen-fixing functions of microbes in urban ecosystems and their contributions to the nitrogen cycle.

Shifts in dominant tree species modulate phyllosphere microbial diversity and function in successional forests

BACKGROUND

Phyllosphere microbiome plays a crucial role in maintaining plant fitness. However, its response to changes in dominant tree species during forest succession still remains poorly understood.

METHODS

In this study, microbial isolation and high-throughput sequencing techniques were used to analyze the community structure and diversity of phyllosphere microbes in pure Pinus massoniana forests, mixed P. massoniana and Liquidambar formosana forests, and pure L. formosana forests.

RESULTS

The results showed that the isolation rates of key plant fungal pathogens varied significantly in phyllosphere across forest types. In pure pine forest, Fusarium was most prevalent in pine needles, while in the mixed forest, Alternaria was dominant. For Liquidambar leaves, Phyllosticta dominated in pure forests, while Colletotrichum was prevalent in the mixed forests. Alpha diversity analysis revealed that higher microbial richness and diversity in the mixed forest compared to the pure forest. The bacterial community structure in Liquidambar leaves differed between the pure forest and the mixed forest. Co-occurrence networks confirmed more complex and stable microbial compositions and interactions in the mixed forest. Bacterial communities in pine needles exhibited higher functional capacity for methanotrophy and nitrogen fixation in the mixed forests.

CONCLUSIONS

The results demonstrate that the mixed forests foster greater microbial diversity, complexity, and functional potential in the phyllosphere compared to the pure forests, highlighting the importance of forest composition in shaping phyllosphere microbial communities.

Unexpected Genetic Diversity of Nostocales (Cyanobacteria) Isolated from the Phyllosphere of the Laurel Forests in the Canary Islands (Spain)

A total of 96 strains of Nostocales (Cyanobacteria) were established from the phyllosphere of the laurel forests in the Canary Islands (Spain) and the Azores (Portugal) using enrichment media lacking combined nitrogen. The strains were characterized by light microscopy and SSU rRNA gene comparisons. Morphologically, most strains belonged to two different morphotypes, termed "Nostoc-type" and "Tolypothrix-type". Molecular phylogenetic analysis of 527 SSU rRNA gene sequences of cyanobacteria (95 sequences established during this study plus 392 sequences from Nostocales and 40 sequences from non-heterocyte-forming cyanobacteria retrieved from the databases) revealed that none of the SSU rRNA gene sequences from the phyllosphere of the laurel forests was identical to a database sequence. In addition, the genetic diversity of the isolated strains was high, with 42 different genotypes (44% of the sequences) recognized. Among the new genotypes were also terrestrial members of the genus Nodularia as well as members of the genus Brasilonema. It is concluded that heterocyte-forming cyanobacteria represent a component of the phyllosphere that is still largely undersampled in subtropical/tropical forests.

The microbial-driven nitrogen cycle and its relevance for plant nutrition

Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition.

Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens

The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.

Foliar nitrogen uptake in broadleaf evergreen Mediterranean forests: Fertilisation experiment with labelled nitrogen

Atmospheric nitrogen (N) deposition in Mediterranean sclerophyllous forests of Holm oak (Quercus rotundifolia, Q. ilex) in Spain often exceeds empirical critical loads established for ecosystem conservation. There are still uncertainties on the capacity of canopy retention and uptake of the atmospheric N deposited of these forests. Studying and analysing all the forest nitrogen-cycle processes is essential to understand the potential effect of N deposition in these ecosystems. This study conducted a year-long short-term fertilisation experiment with labelled ammonium (15N-NH4) and nitrate (15N-NO3) to estimate foliar N absorption rates and assess the influence of leaf phenology and meteorological seasonal variations. Fertilising solutions were prepared to simulate low and high wet N deposition concentration, based on data reported from previous studies. Additionally, ecophysiological and meteorological measurements were collected to explore potential relationships between absorption rates, plant activity, and weather conditions. The results showed that Holm oak leaves were able to absorb both oxidised and reduced N compounds, with higher rates of NH4+ absorption. N recovery of both NH4+ and NO3- was higher in the low concentration treatments, suggesting reduced effectiveness of absorption as concentration increases. Foliar absorption rates were leaf-age dependent, with the highest values observed in young developing leaves. Foliar uptake showed seasonal changes with a clear reduction during the summer, linked to drought and dry weather conditions, and showing also smaller leaf net assimilation and stomatal conductance. During the rest of the year, foliar N absorption was not clearly associated to plant physiological activity but with environmental conditions. Our findings suggest that Holm oak canopies could absorb an important part of the incoming N deposition, but this process is compound, season and leaf phenology dependent. Further research is therefore needed to better understand and model this part of the N cycle.

Harnessing biological nitrogen fixation in plant leaves

The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.

Comparison of the seasonal and successional variation of asymbiotic and symbiotic nitrogen fixation along a glacial retreat chronosequence

Climate change is resulting in accelerated retreat of glaciers worldwide and much nitrogen-poor debris is left after glacier retreats. Asymbiotic dinitrogen (N2) fixation (ANF) can be considered a 'hidden' source of nitrogen (N) for non-nodulating plants in N limited environments; however, seasonal variation and its relative importance in ecosystem N budgets, especially when compared with nodulating symbiotic N2-fixation (SNF), is not well-understood. In this study, seasonal and successional variations in nodulating SNF and non-nodulating ANF rates (nitrogenase activity) were compared along a glacial retreat chronosequence on the eastern edge of the Tibetan Plateau. Key factors regulating the N2-fixation rates as well as the contribution of ANF and SNF to ecosystem N budget were also examined. Significantly greater nitrogenase activity was observed in nodulating species (0.4-17,820.8 nmol C2H4 g-1 d-1) compared to non-nodulating species (0.0-9.9 nmol C2H4 g-1 d-1) and both peaked in June or July. Seasonal variation in acetylene reduction activity (ARA) rate in plant nodules (nodulating species) and roots (non-nodulating species) was correlated with soil temperature and moisture while ARA in non-nodulating leaves and twigs was correlated with air temperature and humidity. Stand age was not found to be a significant determinant of ARA rates in nodulating or non-nodulating plants. ANF and SNF contributed 0.3-51.5 % and 10.1-77.8 %, respectively, of total ecosystem N input in the successional chronosequence. In this instance, ANF exhibited an increasing trend with successional age while SNF increased only at stages younger than 29 yr and then decreased as succession proceeded. These findings help improve our understanding of ANF activity in non-nodulating plants and N budgets in post glacial primary succession.

High-Throughput Absolute Quantification Sequencing Reveals that a Combination of Leguminous Shrubs Is Effective in Driving Soil Bacterial Diversity During the Process of Desertification Reversal

Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.

On the role of the phyllosphere community in leaf wettability and water shedding

We explore the interplay among factors affecting leaf wettability and water shedding by discussing how the phyllosphere directly affects plant wettability.