Nutrient Enrichment Alters Salt Marsh Fungal Communities and Promotes Putative Fungal Denitrifiers

Marsh sediments chronically exposed to nitrogen enrichment contain degraded organic matter that is less vulnerable to decomposition via nitrate reduction

Blue carbon habitats, including salt marshes, can sequester carbon at rates that are an order of magnitude greater than terrestrial forests. This ecosystem service may be under threat from nitrate (NO3-) enrichment, which can shift the microbial community and stimulate decomposition of organic matter. Despite efforts to mitigate nitrogen loading, salt marshes continue to experience chronic NO3- enrichment, however, the long-term consequence of this enrichment on carbon storage remains unclear. To investigate the effect of chronic NO3- exposure on salt marsh organic matter decomposition, we collected sediments from three sites across a range of prior NO3- exposure: a relatively pristine marsh, a marsh enriched to ~70 μmol L-1 NO3- in the flooding seawater for 13 years, and a marsh enriched between 100 and 1000 μmol L-1 for 40 years from wastewater treatment effluent. We collected sediments from 20 to 25 cm depth and determined that sediments from the most chronically enriched site had less bioavailable organic matter and a distinct assemblage of active microbial taxa compared to the other two sites. We also performed a controlled anaerobic decomposition experiment to test whether the legacy of NO3- exposure influenced the functional response to additional NO3-. We found significant changes to microbial community composition resulting from experimental NO3- addition. Experimental NO3- addition also increased microbial respiration in sediments collected from all sites. However, sediments from the most chronically enriched site exhibited the smallest increase, the lowest rates of total NO3- reduction by dissimilatory nitrate reduction to ammonium (DNRA), and the highest DNF:DNRA ratios. Our results suggest that chronic exposure to elevated NO3- may lead to residual pools of organic matter that are less biologically available for decomposition. Thus, it is important to consider the legacy of nutrient exposure when examining the carbon cycle of salt marsh sediments.

The Microbial Ecology of Estuarine Ecosystems

Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.

Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland

Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.

Nutrient loading decreases blue carbon by mediating fungi activities within seagrass meadows

Coastal pollution, including nutrient loading, can negatively impact seagrass health and cover and may consequently alter soil organic carbon (SOC) accumulation and preservation. Key to understanding how eutrophication impacts SOC cycling in seagrass ecosystems is how nutrient loading changes the sources of carbon being deposited and how these changes in resources, both nutrients and carbon availability, influence soil microbiota community and activity. Currently, the direction and magnitude of nutrient loading impacts on seagrass SOC dynamics are poorly understood at a meadow scale, limiting our ability to reveal the driving mechanisms of SOC remineralisation. The purpose of this study was to assess the response of surface SOC and soil microbiomes to nutrient loading within tropical seagrass meadows. To achieve this, we quantified both total SOC and recalcitrant soil organic carbon (RSOC) concentrations and sources, in addition to the composition of bacterial and fungal communities and soil extracellular enzyme activities. We found that nutrient loading elevated SOC and RSOC content, mainly facilitated by enhanced algal growth. There was no nutrient effect on the soil prokaryotic communities, however, saprotrophic fungi groups (i.e. Trapeliales, Sordaridales, Saccharomycetales and Polyporales) and fungal activities were elevated under high nutrient conditions, including extracellular enzyme activities linked to seagrass-based cellulose and lignin decomposition. This relative increase in RSOC transformation may decrease the relative contribution of seagrass carbon to RSOC pools. Additionally, significantly different fungal communities were observed between adjacent T. hemprichii and E. acoroides areas, which coincided with elevated RSOC-decomposing enzyme activity in T. hemprichii meadows, even though the mixed seagrass meadow received allochthonous SOC and RSOC from the same sources. These results suggest that nutrient loading stimulated fungal activity and community shifts specific to the local seagrass species, thereby causing fine-scale (within-meadow) variability in SOC cycling in response to nutrient loading. This study provides evidence that fungal composition and activity, mediated by human activities (e.g. nutrient loading), can be an important influence on seagrass blue carbon accumulation and remineralisation.

Are lulworthioid fungi dark septate endophytes of the dominant Mediterranean seagrass Posidonia oceanica?

A previous study from Sicily, Italy, indicated that the dominant Mediterranean seagrass Posidonia oceanica forms a dark septate endophytic (DSE) association with a lulworthioid fungus ('Lulwoana sp.'). This conflicts with several other studies from the NW Mediterranean Sea that point at the recently described pleosporalean fungus Posidoniomyces atricolor. I collected P. oceanica roots at eight sites around Sicily and checked them for fungal colonization using light microscopy. At three sites, root fungal symbionts (mycobionts) were isolated into pure cultures and identified using ITS rDNA sequences. Posidoniomyces atricolor represented the most frequent mycobiont (56 isolates), closely followed by lulworthioid fungi (51). The obtained mycobiont spectrum also included Cladosporium (2), Alternaria (1), Corollospora (1), Fusarium (1), Penicillium (1) and Vishniacozyma (1) isolates. The characteristic DSE root colonization, similar to those occurring in terrestrial plants but not known from any other seagrass, was found in all investigated P. oceanica individuals. The microscopy screening suggests that P. atricolor is responsible for the observed DSE colonization. This study extends the known range of Pos. atricolor and the DSE association characteristic for P. oceanica to the southern Tyrrhenian Sea/Sicily. While lulworthioid fungi regularly occur in P. oceanica tissues, including terminal fine roots, their significance and functioning (e.g. parasitic, pathogenic, endophytic) are unknown and require further investigation. However, there is currently no proof that they belong among dark septate endophytes of this seagrass.

Long-Term Fertilization Alters Nitrous Oxide Cycling Dynamics in Salt Marsh Sediments

Salt marsh sediments are known hotspots for nitrogen cycling, including the production and consumption of nitrous oxide (N₂O), a potent greenhouse gas and ozone-depleting agent. Coastal eutrophication, particularly elevated nitrogen loading from the application of fertilizers, is accelerating nitrogen cycling processes in salt marsh sediments. Here, we examine the impact of long-term fertilization on nitrogen cycling processes with a focus on N₂O dynamics in a New England salt marsh. By combining ¹⁵N-tracer experiments with numerical modeling, we found that both nitrification and denitrification contribute to net N₂O production in fertilized sediments. Long-term fertilization increased the relative importance of nitrification to N₂O production, likely a result of increased oxygen penetration from nutrient-induced increases in marsh elevation. Substrate utilization rates of key nitrogen cycling processes revealed links between functions and the corresponding microbial communities. Higher specific substrate utilization rates leading to N₂O production from nitrification in fertilized sediments indicate a shift in the community composition of ammonia oxidizers, whereas the lack of change in specific substrate utilization of N₂O production from denitrification under long-term fertilization suggests resilience of the denitrifying communities. Both are consistent with previous studies on the functional gene community composition in these experimental plots.

Diversity and N2O Production Potential of Fungi in an Oceanic Oxygen Minimum Zone

Fungi in terrestrial environments are known to play a key role in carbon and nitrogen biogeochemistry and exhibit high diversity. In contrast, the diversity and function of fungi in the ocean has remained underexplored and largely neglected. In the eastern tropical North Pacific oxygen minimum zone, we examined the fungal diversity by sequencing the internal transcribed spacer region 2 (ITS2) and mining a metagenome dataset collected from the same region. Additionally, we coupled ¹⁵N-tracer experiments with a selective inhibition method to determine the potential contribution of marine fungi to nitrous oxide (N₂O) production. Fungal communities evaluated by ITS2 sequencing were dominated by the phyla Basidiomycota and Ascomycota at most depths. However, the metagenome dataset showed that about one third of the fungal community belong to early-diverging phyla. Fungal N₂O production rates peaked at the oxic–anoxic interface of the water column, and when integrated from the oxycline to the top of the anoxic depths, fungi accounted for 18–22% of total N₂O production. Our findings highlight the limitation of ITS-based methods typically used to investigate terrestrial fungal diversity and indicate that fungi may play an active role in marine nitrogen cycling.

Not All Nitrogen Is Created Equal: Differential Effects of Nitrate and Ammonium Enrichment in Coastal Wetlands

Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3-) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3- can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3- to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.