New soil organic matter (SOM) models highlight the role of microorganisms in plant litter decomposition and storage of microbial-derived carbon (C) molecules. Wetlands store more C per unit area than ...any other ecosystem, but SOM storage mechanisms such as aggregation and metal complexes are mostly untested in wetlands. This review discusses what is currently known about the role of microorganisms in SOM formation and C sequestrations, as well as, measures of microbial communities as they relate to wetland C cycling. Studies within the last decade have yielded new insights about microbial communities. For example, microbial communities appear to be adapted to short-term fluctuations in saturation and redox and researchers have observed synergistic pairings that in some cases run counter to thermodynamic theory. Significant knowledge gaps yet to be filled include: (i) What controls microbial access to and decomposition of plant litter and SOM? (ii) How does microbial community structure shape C fate, across different wetland types? (iii) What types of plant and microbial molecules contribute to SOM accumulation? Studies examining the active microbial community directly or that utilize multi-pronged approaches are shedding new light on microbial functional potential, however, and promise to improve wetland C models in the near future.
Fungal endophytes can improve plant tolerance to abiotic stress. However, the role of these plant-fungal interactions in invasive species ecology and their management implications remain unclear. ...This study characterized the fungal endophyte communities of native and invasive lineages of Phragmites australis and assessed the role of dark septate endophytes (DSE) in salt tolerance of this species. We used Illumina sequencing to characterize root fungal endophytes of contiguous stands of native and invasive P. australis along a salinity gradient. DSE colonization was assessed throughout the growing season in the field, and effects of fungal inoculation on salinity tolerance were investigated using laboratory and greenhouse studies. Native and invasive lineages had distinct fungal endophyte communities that shifted across the salinity gradient. DSE colonization was greater in the invasive lineage and increased with salinity. Laboratory studies showed that DSE inoculation increased P. australis seedling survival under salt stress; and a greenhouse assay revealed that the invasive lineage had higher aboveground biomass under mesohaline conditions when inoculated with a DSE. We observed that P. australis can establish mutualistic associations with DSE when subjected to salt stress. This type of plant-fungal association merits further investigation in integrated management strategies of invasive species and restoration of native Phragmites.
High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines ...have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate “Quantitative Sequencing” (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.
Organic matter is sometimes added to soil in wetland mitigation projects, putatively to improve restoration outcomes. At a freshwater mitigation wetland, built in a former agricultural field to ...compensate for development-related wetland losses elsewhere, we conducted a manipulative field experiment using organic matter amendments to identify the effects different types and loading rates had on the development of soil (organic matter, bulk density, and hydric soil indicators), vegetation (root and shoot biomass, floristic quality), and methane (CH
4
) emissions. The amendments included cow manure, composted wood chips, and hay at various loading rates, and municipal wastewater Class A biosolids. We found that there were trade-offs in desired restoration outcomes. Experimental loading rates of hay (226 m
3
ha
−1
) and manure (339 and 678 m
3
ha
−1
) produced more CH
4
(78–92 g m
−2
year
−1
) than unamended plots (28 g m
−2
year
−1
). These same amendments had little effect on hydric soil indicators (e.g., redox potential and reduced iron). Manure almost doubled vegetation biomass (937 g m
−2
versus 534 g m
−2
) compared to the unamended control, largely due to the growth of
Typha
sp. (cattail), an undesired plant at this site that resulted in lower floristic quality. Compared to unamended soils, only wood chips appeared to increase soil organic matter after one growing season. All amendments tended to reduce soil bulk density and penetration resistance, but these were not correlated with root growth. Unexpectedly, hydrology varied considerably due to patchy soil characteristics, despite little variation in elevation – this strongly influenced on our results. We qualitatively observed that constantly inundated plots had lower CH
4
emissions than areas with wet-dry cycles and that cattail proliferated mostly in wetter areas. Contrary to the prescription of organic matter amendments as a method for accelerating soil and vegetation development in wetland restoration projects, our findings demonstrate that amendments may not be necessary to support vegetation and hydric soil development and might unnecessarily exacerbate atmospheric warming and contribute to invasive species spread.
Agriculture, by its intentional design, manipulates the ecological functions of soils. It does so by altering carbon and nutrient inputs; by controlling the plant community; and in the case of ...tillage, by physically disrupting and redistributing the soil within the soil profile. While there are many studies that contrast soil microbiomes across farming systems, few studies have examined the effect of farming system on the vertical organization of taxa in the soil profile. We hypothesized that large effects of farming systems on edaphic factors would lead to large impacts on the microbial community that would reflect the underlying life history strategy of the microbes. For example, that tillage would increase the proportion of unicellular fungi. Our study compared farming systems that had been in place for 13 years in the mid-Atlantic region of the United States. Each system is a 3-year rotation of corn (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum), managed with either conventional no-till, conventional chisel-till, or using organic methods. We determined the relative effect of long-term farming system management on edaphic factors and the soil microbial community with depth structured sampling (0–5, 5–10, 10-Ap, Ap-30 cm). We found relatively small effects of farming system but substantial effects of depth on edaphic factors and microbial communities. For example, differences in management resulted in subtle differences in %C above the Ap horizon. Fungal gene abundance increased in the organic system relative to the no-till system, although neither fungal nor bacterial richness differed across farming systems. Farming system effects on microbial community composition were greatest in the top 10 cm but did not affect the abundance of unicellular fungi. Several groups including Pseudomonas and Mortierellomycota appear to be sensitive to redistribution by tillage in the organic system, but it is not clear to what extent this effect is due to legacy DNA from tillage.
Thirteen-year management of organic and conventional grain farming systems results in modest differences to microbial communities along soil depth profiles1)Organic treatment results in a increase in soil %C and differences in %C depth distribution2)No difference in richness and evenness among farming systems3)A 30 cm depth profile represents a much greater environmental gradient for microbial abundance and diversity than differences among long-term row-crop farming systems that differ in tillage, fertility and pest management Display omitted
•Depth had larger effect than farming system on microbial community.•Farming system effects were concentrated in top 10 cm.•Farming systems altered the distribution of some taxa across depth increments.•No effect of farming system on abundance of unicellular fungi.
1. The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding ...of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. 2. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. 3. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit OTU abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus, 17 Plethodon glutionosus, 10 Plethodon cylindraceus) at three localities to differntiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient (n = 50, 700-1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. 4. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, betadiversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% (SD ± 8.5) per salamander. All salamanders tested negative for Bd. 5. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.
It is increasingly clear that hydrology, vegetation, and soil characteristics are important in controlling methane (CH
4
) emissions from wetlands. However, few studies have examined CH
4
emissions ...between wetland habitats dominated by different plants, or between naturally occurring and restorred wetlands, which are hoped to offer a means of sequestering carbon (C) and offsetting greenhouse gas emission. Our goal was to assess the variation of CH
4
fluxes between different habitats in natural and restored tidal freshwater wetlands. One natural site with three habitats (low marsh, high marsh, and swamp habitat) and restored site with two habitats (low and high marsh) were selected. Both sites are tidal freshwater wetlands (measured salinity <0.3 Practical Salinity Units (PSU)) located on the Patuxent River, Maryland, USA. Gas flux was quantified using static chambers once a month during day and night from May to August 2016 during a single growing season. At 12.5 and 40 cm soil depth, soil redox potential, temperature, porewater CH
4
, and total iron (Fe) concentrations were measured on the same days as flux. Restored habitats had significantly higher soil redox potential (i.e., less reducing conditions) than their natural counterparts (
P
< 0.05). Methane flux had high spatiotemporal variations across natural and restored wetland habitats (ranged from −87,901 mg CH
4
m
−2
day
−1
in restored high marsh during June to 6860 mg CH
4
m
−2
day
−1
in natural swamp habitat during May). Moreover, natural wetland habitats, on average, were significantly warmer (
P
< 0.05) than their restored counterparts at both soil depths (12.5 and 40 cm), where porewater CH
4
concentrations had positive and significant correlation with wetland soil temperatures (r = 0.36 and
P
< 0.001 – the warmer the soil, the higher the porewater CH
4
available). For a more precise global C budget, soil temperature, spatiotemporal CH
4
variations between wetland types, and tidal effects should be considered in accounting for CH
4
fluxes in wetlands in general and tidal freshwater wetlands specifically.
Tidal wetlands, such as tidal marshes and mangroves, are hotspots for carbon sequestration. The preservation of organic matter (OM) is a critical process by which tidal wetlands exert influence over ...the global carbon cycle and at the same time gain elevation to keep pace with sea-level rise (SLR). The present study assessed the effects of temperature and relative sea level on the decomposition rate and stabilization of OM in tidal wetlands worldwide, utilizing commercially available standardized litter. While effects on decomposition rate per se were minor, we show strong negative effects of temperature and relative sea level on stabilization, as based on the fraction of labile, rapidly hydrolyzable OM that becomes stabilized during deployment. Across study sites, OM stabilization was 29 % lower in low, more frequently flooded vs. high, less frequently flooded zones. Stabilization declined by ∼ 75 % over the studied temperature gradient from 10.9 to 28.5 ∘C. Additionally, data from the Plum Island long-term ecological research site in Massachusetts, USA, show a pronounced reduction in OM stabilization by > 70 % in response to simulated coastal eutrophication, confirming the potentially high sensitivity of OM stabilization to global change. We therefore provide evidence that rising temperature, accelerated SLR, and coastal eutrophication may decrease the future capacity of tidal wetlands to sequester carbon by affecting the initial transformations of recent OM inputs to soil OM.
Summary
This study determined nitrification activity and nitrifier community composition in soils under stands of red alder (Alnus rubra) and Douglas fir (Pseudotsuga menziesii) at two sites in ...Oregon. The H.J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon, has low net N mineralization and gross nitrification rates. Cascade Head Experimental Forest, in the Coast Range, has higher net N mineralization and nitrification rates and soil pH is lower. Communities of putative bacterial ammonia‐oxidizing bacteria (AOB) and archaeal ammonia‐oxidizing archaea (AOA) ammonia oxidizers were examined by targeting the gene amoA, which codes for subunit A of ammonia monooxygenase. Nitrification potential was significantly higher in red alder compared with Douglas‐fir soil and greater at Cascade Head than H.J. Andrews. Ammonia‐oxidizing bacteria amoA genes were amplified from all soils, but AOA amoA genes could only be amplified at Cascade Head. Gene copy numbers of AOB and AOA amoA were similar at Cascade Head regardless of tree type (2.3–6.0 × 106amoA gene copies g−1 of soil). DNA sequences of amoA revealed that AOB were members of Nitrosospira clusters 1, 2 and 4. Ammonia‐oxidizing bacteria community composition, determined by terminal restriction fragment length polymorphism (T‐RFLP) profiles, varied among sites and between tree types. Many of the AOA amoA sequences clustered with environmental clones previously obtained from soil; however, several sequences were more similar to clones previously recovered from marine and estuarine sediments. As with AOB, the AOA community composition differed between red alder and Douglas‐fir soils.
Urea-N is ubiquitous in soils, having both natural and anthropogenic sources. The enzyme urease catalyzes its hydrolysis to NH3 and is produced by plants and many soil microorganisms, but there are ...growing concerns related to possible urea-induced eutrophication of surface waters proximate to agricultural fields. Agronomic research has focused on the relationship between urea hydrolysis and soil physical or chemical properties, rather than on direct measurements of the microbial community and its population diversity, especially using quantification of genes that code for urease. We quantified bacterial and archaeal 16S rRNA, fungal ITS, and bacterial ureC gene copies as a function of physical and chemical soil properties. Soils were sampled from A and B horizons along a toposequence that comprised an agricultural field, a grassed field border, and a forested riparian zone in the Chesapeake Bay watershed of Maryland. The riparian zone soils contained the highest total number of genes among both A- and B-horizon soils. The soils were then experimentally altered in the laboratory to achieve a range of pH values between 3.1 and 7.1. Soil pH was chosen as a variable because it varies both naturally and due to agronomic practices, and it influences microbial community structure and function. Archaeal 16S rRNA extracted from the pH-adjusted soils did not show a consistent pattern of increase or decrease with changes in pH, while ITS was greatest at low pH and bacterial 16S and bacterial ureC were greatest at high pH. We measured higher urea hydrolysis rates and gene copy numbers in A-horizon soils than in B-horizon soils, and found that urea hydrolysis rate was significantly correlated with gene copies of bacterial 16S, ureC, and increased pH. This suggests that liming acid soils increases urea hydrolysis rates in part by encouraging the growth of microorganisms capable of producing urease.
•pH impacts urease gene numbers.•Bacterial urease gene numbers are correlated with urea hydrolysis rate.•1–20% of bacterial community was ureolytic in the studied soils.•No correlation found between archaeal 16S gene copy number and urea hydrolysis rate.•No correlation found between fungal ITS gene copy number and urea hydrolysis rate.
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