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1. Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay

   https://doi.org/10.1186/s40793-021-00392-z  

   Wang, Hualong ; Chen, Feng ; Zhang, Chuanlun ; Wang, Min ; Kan, Jinjun ( November 2021 , Environmental Microbiome)

   Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries.

   Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chla, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the ‘small world’ (a group of more interconnected species), network stability, and habitat partitioning/preferences.

   Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.

    

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2. Facilitation strength across environmental and beneficiary trait gradients in stream communities

   https://doi.org/10.1111/1365-2656.13992  

   Tumolo, Benjamin B. ; Albertson, Lindsey K. ; Daniels, Melinda D. ; Cross, Wyatt F. ; Sklar, Leonard L. ( August 2023 , Journal of Animal Ecology)

   Ecosystem engineers modify habitats in ways that facilitate other community members by ameliorating harsh conditions. The strength of such facilitation is predicted to be influenced by both beneficiary traits and abiotic context. One key trait of animals that could control the strength of facilitation is beneficiary body size because it should determine how beneficiaries fit within and exploit stress ameliorating habitat modifications. However, few studies have measured how beneficiary body size relates to facilitation strength along environmental gradients.

   We examined how the strength of facilitation by net‐spinning caddisflies on invertebrate communities in streams varied along an elevation gradient and based on traits of the invertebrate beneficiaries. We measured whether use of silk retreats as habitat concentrated invertebrate density and biomass compared to surrounding rock surface habitat and whether the use of retreat habitat varied across body sizes of community members along the gradient.

   We found that retreats substantially concentrated the densities of a diversity of taxa including eight different Orders, and this effect was greatest at high elevations. Caddisfly retreats also concentrated invertebrate biomass more as elevation increased. Body size of invertebrates inhabiting retreats was lower than that of surrounding rock habitats at low elevation sites, however, body size between retreats and rocks converged at higher elevation sites. Additionally, the body size of invertebrates found in retreats varied within and across taxa. Specifically, caddisfly retreats functioned as a potential nursery for taxa with large maximal body sizes. However, the patterns of this taxon‐specific nursery effect were not influenced by elevation unlike the patterns observed based on community‐level body size.

   Collectively, our results indicate that invertebrates use retreats in earlier life stages or when they are smaller in body size independent of life stage. Furthermore, our analysis suggests that facilitation strength intensifies as elevation increases within stream invertebrate communities.

   Further consideration of how trait variation and environmental gradients interact to determine the strength and direction of biotic interactions will be important as species ranges and environmental conditions continue to shift.

    

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3. Floral and pollinator functional diversity mediate network structure along an elevational gradient

   https://doi.org/10.1007/s00035-024-00308-w  

   Aguirre, Luis A. ; Junker, Robert R. ( March 2024 , Alpine Botany)

   Elevational gradients in alpine ecosystems are well suited to study how plant and pollinator communities respond to climate change. In the Austrian Alps, we tested how the taxonomic and functional diversity of plants and their pollinators change with increasing elevation and how this affects plant–pollinator network structure. We measured the phenotypes of flowering plants and their pollinators and observed their interactions in 24 communities along an elevational gradient. To assess variation in floral and pollinator traits, we then quantified trait spaces (n-dimensional hypervolumes) occupied by flowers and pollinators in each community. To assess plant–pollinator network structure, we quantified the levels of complementary specialization (H₂’), modularity and nestedness (weighted NODF) for each community. As elevation increased, most measures of diversity and network specialization either declined linearly or in an oscillating manner. Communities that exhibited higher pollinator functional diversity exhibited larger degrees of complementary specialization and modularity; and communities with greater floral and pollinator functional diversity and higher phylogenetic diversity were less nested. Altogether, the degree to which elevation, species diversity, functional diversity and network structure changed in conjunction suggests environmental effects on the functional and phylogenetic diversity of plants and pollinators and consequently network structure. Our results suggest that the effects of climate change on plant and pollinator community composition will impact plant–pollinator network structure and potentially pollination services at the community scale.

    

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4. Can dynamic network modelling be used to identify adaptive microbiomes?

   https://doi.org/10.1111/1365-2435.13491  

   Garcia, Joshua ; Kao‐Kniffin, Jenny ; Bennett, ed., Alison ( December 2019 , Functional Ecology)

   In recent times, interest has grown in understanding how microbiomes – the collection of microorganisms in a specific environment – influence the survivability or fitness of their plant and animal hosts. The profound diversity of bacterial and fungal species found in certain environments, such as soil, provides a large pool of potential microbial partners that can interact in ways that reveal patterns of associations linking host–microbiome traits developed over time. However, most microbiome sequence data are reported as a community fingerprint, without analysis of interaction networks across microbial taxa through time.

   To address this knowledge gap, more robust tools are needed to account for microbiome dynamics that could signal a beneficial change to a plant or animal host. In this paper, we discuss applying mathematical tools, such as dynamic network modelling, which involves the use of longitudinal data to study system dynamics and microbiomes that identify potential alterations in microbial communities over time in response to an environmental change. In addition, we discuss the potential challenges and pitfalls of these methodologies, such as handling large amounts of sequencing data and accounting for random processes that influence community dynamics, as well as potential ways to address them.

   Ultimately, we argue that components of microbial community interactions can be characterized through mathematical models to reveal insights into complex dynamics associated with a plant or animal host trait. The inclusion of interaction networks in microbiome studies could provide insights into the behaviour of complex communities in tandem with host trait modification and evolution.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

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5. Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem

   https://doi.org/10.7717/peerj.3377  

   Geyer, Kevin M. ; Takacs-Vesbach, Cristina D. ; Gooseff, Michael N. ; Barrett, John E. ( January 2017 , PeerJ)

   Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability) and geochemical severity (e.g., pH, electrical conductivity). In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP) exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM) fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol O 2 /m 2 /s in the most arid soils to an average of 6.97 μmol O 2 /m 2 /s in the most productive soils, the latter equivalent to 217 g C/m 2 /y in annual NPP assuming a 60 day growing season. A diversity index of four carbon-acquiring enzyme activities also increased with soil productivity, suggesting that the diversity of organic substrates in mesic environments may be an additional driver of microbial diversity. Overall, soil productivity was a stronger predictor of microbial diversity and enzymatic activity than any estimate of geochemical severity. These results highlight the fundamental role of environmental gradients to control community diversity and the dynamics of ecosystem-scale carbon pools in arid systems. 

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