Interwoven processes in fish development: microbial community succession and immune maturation

Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.

Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution

In this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and functions from an energetic perspective, by outlining relevant thermodynamic theory relating to molecular, metabolic, cellular, individual, population, species, ecosystem and biome organization. We next investigate the fundamental relationships between systems theory and thermodynamics in terms of the Earth system, examining the key characteristics of self-assembly, self-organization (including autonomy), emergence, non-linearity, feedback and sub-optimality. Finally, we examine the relevance of systems theory and thermodynamics with reference to two specific aspects: the tempo and directionality of evolution and the directional and predictable process of ecological succession. We discuss the importance of the entropic drive in understanding altruism, multicellularity, mutualistic and antagonistic relationships and how maximum entropy production theory may explain patterns thought to evidence the intermediate disturbance hypothesis.

The glacier melting process is an invisible barrier to the development of Antarctic subtidal macroalgal assemblages

Ecological macroalgal succession in glacier-free areas has remained at the pioneer seral stage despite six decades of glacial retreat at Marian Cove, King George Island, Antarctica. With the rapid melting of glaciers in the West Antarctic Peninsula owing to global warming, a massive amount of meltwater is flowing into the coast, creating marine environmental gradients such as turbidity, water temperature, and salinity. This study examined the spatial and vertical distributions (up to a depth of 25 m) of macroalgal assemblages from nine sites in Maxwell Bay and Marian Cove. The macroalgal assemblages were analyzed for six sites located 0.2, 0.8, 1.2, 2.2, 3.6, and 4.1 km away from the glacier, including three sites where the glacial retreat history of Marian Cove could be estimated. To investigate the effects of meltwater, differences in the coastal environment were analyzed based on data collected from five stations located 0.4, 0.9, 3.0, 4.0, and 5.0 km away from the glacier. The macroalgal assemblages and marine environment were divided into two groups-inside and outside the cove-based on the region 2-3 km away from the glacier, which has been ice-free since 1956 and shows significant differences. In the three sites near the glacier front, Palmaria decipiens was dominant, and three to four species were distributed, whereas in the two sites outside the cove, nine and 14 species appeared, respectively, similar to the assemblage of the other three sites in Maxwell Bay. Palmaria decipiens, a representative opportunistic pioneer species in Antarctica, is dominant because of its physiological adaptation despite the high turbidity and low water temperature of the glacier front. This study shows that macroalgal assemblages in Antarctic fjord-like coves respond to glacial retreat and are valuable in understanding the macroalgal succession in Antarctica.

Changes in Coleopteran assemblages over a successional chronosequence in a Mexican tropical dry forest

Coleopterans are the most diverse animal group on Earth and constitute good indicators of environmental change. However, little information is available about Coleopteran communities' responses to disturbance and land-use change. Tropical dry forests have undergone especially extensive anthropogenic impacts in the past decades. This has led to mosaic landscapes consisting of areas of primary forest surrounded by pastures, agricultural fields and secondary forests, which negatively impacts many taxonomic groups. However, such impacts have not been assessed for most arthropod groups. In this work, we compared the abundance, richness and diversity of Coleopteran morphospecies in four different successional stages in a tropical dry forest in western Mexico, to answer the question: How do Coleopteran assemblages associate with vegetation change over the course of forest succession? In addition, we assessed the family composition and trophic guilds for the four successional stages. We found 971 Coleopterans belonging to 107 morphospecies distributed in 28 families. Coleopteran abundance and richness were greatest for pastures than for latter successional stages, and the most abundant family was Chrysomelidae, with 29% of the individuals. Herbivores were the most abundant guild, accounting for 57% of the individuals, followed by predators (22%) and saprophages (21%) beetles. Given the high diversity and richness found throughout the successional chronosequence of the studied tropical dry forest, in order to have the maximum number of species associated with tropical dry forests, large tracts of forest should be preserved so that successional dynamics are able to occur naturally.

Land abandonment as driver of woody vegetation dynamics in Tamaulipan thornscrub at Northeastern Mexico

Background

Vegetation structure is defined as the temporal and spatial distribution of plant species in a particular site. Vegetation structure includes vertical and horizontal distribution and has been widely used as an indicator of successional changes. Ecological succession plays an essential role in the determination of the mechanisms that structure plant communities under anthropogenic disturbances. After an anthropogenic disturbance, such as grazing, forests follow changes in the original composition and vegetation structure, which eventually could restore some of their attributes to become mature forests again. To know how the time of abandonment affects woody plant communities, we ask the following questions: (1) How does the species richness, diversity, and vertical structure (A index) change concerning the time of abandonment? (2) Are species similarities among woody vegetation communities determined by land abandonment? (3) Which woody species have the highest ecological importance in each successional stage?

Methods

We explored how successional stages after land abandonment mediated the species richness, species diversity (alpha and beta), and ecological importance value index on four areas of Tamaulipan thornscrub. We selected four areas that differed in time of abandonment: 10, 20, 30, and >30 years. The first three areas were used for cattle grazing, whereas the >30-year area was selected as a control since it does not have a record of disturbance by cattle grazing or agriculture. During the summer of 2012, we randomly established four square plots (40 m × 40 m) in each area, separated at least 200 m from each other. In each plot, we recorded all woody individuals per species with a basal diameter ≥1 cm at 10 cm above ground level. We estimated species richness indices, species diversity (alpha and beta), and ecological importance value index.

Results

We recorded 27 woody species belonging to 23 genera and 15 families. Fabaceae accounted for 40% of the species. Acacia farnesiana was the most important and abundant species in the first three successional stages. We suggested that older successional stages of Tamaulipan thornscrub promote woody plant communities, characterized by a higher complex structure than younger communities. We observed the highest species similarity between the sites with a closer time of abandonment, while the lowest similarity was shown between the sites with extreme time of abandonment. We conclude that Tamaulipan thornscrub shows a similar trend of ecological succession to other dry forests and the time of abandonment has a high mediation on plant dynamics in the Tamaulipan thornscrub. Also, we stand out the importance of secondary forests for Tamaulipan thornscrub woody plant communities. Finally, we recommended future studies include aspects of regeneration speed, the proximity of mature vegetation, and the interactions of plants with their seed dispersers.

How feedback loops between meso- and macrofauna and organic residues contrasting in chemical quality determine decomposition dynamics in soils

The concept of feedback loops between changes in chemical quality of decomposing organic residues and changes in faunal communities was employed in studying how such feedback loops, representing distinct ecological successional stages, determine decomposition dynamics in soils. A 52-week litterbag decomposition study was superimposed onto an 18-year long term field experiment. Four types of organic residues contrasting in chemical quality (i.e., nitrogen (N), lignin, polyphenols, cellulose) were incorporated into soil annually to assess decomposition and associated meso- and macrofauna communities. In the first 4 weeks after residue incorporation (loop #1), the abundances (densities) of both mesofauna and macrofauna were positively influenced by labile cellulose and N. The mesofauna Collembola and Acari contributed 70-100% and 0-30% to the decomposition, respectively, while the macrofauna beetles and flies contributed 20-90% and 10-66%, respectively. The abundances were highest under groundnut (high N, low lignin) ([1.35 and 0.85 individual number (g dry litter)^-1] for mesofauna and macrofauna, respectively). The presence of macrofauna at week 2 led to a mass loss (R² = 0.67**), indicating that macrofauna preceded mesofauna in degrading residue. In week 8 (transition of loop #2 to #3), only macrofauna (beetles dominated contributing 65%) played an important role in lignin decomposition (R² = 0.56**), resulting in a mass loss (R² = 0.52**). In week 52 (loop #4) macrofauna, ants (Formicidae) replaced beetles as the dominant decomposers showing a feedback reaction to availability of protected cellulose. The Formicidans contributed 94% to the decomposition and influenced losses of mass (R² = 0.36*) and N (R² = 0.78***). The feedback loop concept provides a more comprehensive "two-sided" view into decomposition, as regulated simultaneously by two factors, than earlier "one-sided" approaches to soil fauna-mediated decomposition.

Population synchrony indicates functional connectivity in a threatened sedentary butterfly

Dispersal is a key influence on species' persistence, particularly in the context of habitat fragmentation and environmental change. Previously, residual population synchrony has been demonstrated to be an effective proxy for dispersal in mobile butterflies (Powney et al. 2012). Here, we highlight the utility and limitations of population synchrony as an indicator of functional connectivity and persistence, at a range of spatial scales, in a specialist, sedentary butterfly. While at the local scale, population synchrony is likely indicative of dispersal in the pearl-bordered fritillary, Boloria euphrosyne, over larger scales, habitat is likely to influence population dynamics. Although declines in local-scale synchrony conformed to typical movement in this species, synchrony showed no significant trend with distance when studied at larger (between-site) scales. By focusing on specific site comparisons, we draw the conclusion that heterogeneity in habitat successional stage drives asynchrony between sites at larger distances and is, therefore, likely to be a more important driver of population dynamics over large distances than dispersal. Within-site assessments of synchrony highlight differences in dispersal based on habitat type, with movement shown to be most inhibited between transect sections with contrasting habitat permeability. While synchrony has implications for metapopulation stability and extinction risk, no significant difference was found in average site synchrony between sites that had gone extinct during the study period and those remaining occupied. We demonstrate that population synchrony may be used to assess local-scale movement between sedentary populations, as well as to understand barriers to dispersal and guide conservation management.

Ecological succession and the competition-colonization trade-off in microbial communities

BACKGROUND

During range expansion in spatially distributed habitats, organisms differ from one another in terms of their patterns of localization versus propagation. To exploit locations or explore the landscape? This is the competition-colonization trade-off, a dichotomy at the core of ecological succession. In bacterial communities, this trade-off is a fundamental mechanism towards understanding spatio-temporal fluxes in microbiome composition.

RESULTS

Using microfluidics devices as structured bacterial habitats, we show that, in a synthetic two-species community of motile strains, Escherichia coli is a fugitive species, whereas Pseudomonas aeruginosa is a slower colonizer but superior competitor. We provide evidence highlighting the role of succession and the relevance of this trade-off in the community assembly of bacteria in spatially distributed patchy landscapes. Furthermore, aggregation-dependent priority effects enhance coexistence which is not possible in well-mixed environments.

CONCLUSIONS

Our findings underscore the interplay between micron-scale landscape structure and dispersal in shaping biodiversity patterns in microbial ecosystems. Understanding this interplay is key to unleash the technological revolution of microbiome applications.

Corpse decay of wild animals leads to the divergent succession of nrfA-type microbial communities

Animal carcasses introduce large amounts of nitrates and ammonium into the soil ecosystem. Some of this ammonium is transformed from nitrite through the nrfA-type microbial community. However, it is unclear how nrfA-type microorganisms respond to the decomposition of corpses. This study applied high-throughput sequencing to characterize the ecological succession of nrfA-type microbial communities in grassland soil. Our results showed that Cyclobacterium and Trueperella were the predominant genera for nrfA-type communities in soil with a decomposing corpse (experimental group), while Cyclobacterium and Archangium were dominant in soil without a corpse (control group). The alpha diversity indexes and the resistance and resilience indexes of the microbial communities initially increased and then decreased during decomposition. Compared with the control group, nrfA-encoding community structure in the experimental group gradually became divergent with succession and temporal turnover accelerated. Network analysis revealed that the microbial communities of the experimental group had more complex interactions than those of the control groups. Moreover, the bacterial community assembly in the experimental group was governed by stochastic processes, and the communities of the experimental group had a weaker dispersal capacity than those of the control group. Our results reveal the succession patterns of the nrfA-type microbial communities during degradation of wild animal corpses, which can offer references for demonstrating the ecological mechanism underlying the changes in the nrfA-type microbial community during carcass decay. KEY POINTS: • Corpse decay accelerates the temporal turnover of the nrfA-type community in soil. • Corpse decay changes the ecological succession of the nrfA-type community in soil. • Corpse decay leads to a complex co-occurrence pattern of the nrfA-type community in soil.

Broader environmental adaptation of rare rather than abundant bacteria in reforestation succession soil

Revealing the responses of rare and abundant bacteria to environmental change is crucial for understanding microbial community assembly and ecosystem function. However, both the environmental adaptability and the ecological assembly processes exhibited by rare and abundant soil bacteria remain poorly understood. Here we investigated the assembly processes of rare and abundant bacteria along a chronosequence of a 35-year reforestation succession (8, 17, and 35 years), particularly with regard to their environmental adaptations. Compared to the abundant taxa, the phylogenetic clustering of rare taxa was tighter but their environmental breadth wider. Homogeneous selection (65.8%) belonging to deterministic processes dominated the rare bacterial assembly, whereas homogenizing dispersal and undominated process (57.9%) belonging to stochastic processes governed the abundant taxa. Neutral processes had a significant impact on shaping the rare taxa compared to the abundant taxa. Rare taxa were environmentally less constrained than abundant taxa. Soil EC was the major determinant factor for the assembly processes of both rare and abundant taxa. Ecological assembly processes showed a significant negative correlation with rare bacterial functional redundancies, while they had a significant positive correlation with the abundant taxa. Microbial network modularity further demonstrated that rare taxa developed stronger environmental adaptation strategies than their abundant counterparts. Our study significantly advances the knowledge of the environmental adaptability of rare and abundant bacteria and emphasizes their key role in reforestation ecological succession soils.

Does invasion by Pteridium aquilinum (Dennstaedtiaceae) affect the ecological succession in Atlantic Forest areas after a fire?

Pteridium aquilinum (Dennstaedtiaceae) colonization affects ecological and restoration processes. The knowledge of the impacts on the ecological succession by this species allows the use of restoration strategies in invaded environments. This work aimed to evaluate the floristic composition, diversity, structure, density, basal area, height, and diameter of natural regeneration in three areas of the Atlantic Forest in the Serra do Espinhaço Biosphere Reserve in an area invaded by P. aquilinum after a fire. Three environments with different coverage intensities by P. aquilinum were studied, and the plants over 10 cm in height or 5 cm in canopy diameter were measured. The floristic composition and diversity were analyzed using indices presented by Chao, Fisher, Margalef, Pielou, Shannon-Weaver, and Simpson, and similarity was evaluated by the Jaccard index. Species density, basal area, height, and canopy diameter classes were also evaluated. The floristic composition, diversity, structure of natural regeneration, density, and basal area were higher in post-fire areas with a lower coverage by P. aquilinum. The topsoil coverage with plant litter and the possible effect of P. aquilinum allelopathy probably reduced the species richness and diversity. The proportion of plants from the lowest height and canopy diameter classes was higher under moderate coverage by P. aquilinum. The reduction in the floristic composition, diversity, number of species, and basal area in post-fire areas colonized by P. aquilinum is probably due to this species aggressiveness. The population of this plant is high, accumulating large quantities of plant litter as a physical barrier preventing light and propagules from reaching the soil, reducing the germination of the seed bank and, consequently, the natural regeneration. The floristic composition, diversity, structure of natural regeneration, density, and basal area were lower in areas with higher coverage by P. aquilinum. The proportion of plants in the most significant height and canopy diameter classes was higher with reduced coverage by P. aquilinum. The P. aquilinum reduced forest succession in areas after a fire.

Can reed harvest be used as a management strategy for improving invertebrate biomass and diversity?

The succession-driven reed bed habitat hosts a unique flora and fauna including several endangered invertebrate species. Reed beds can be managed through commercial winter harvest, with implications for reed bed conservation. However, the effects of winter harvest on the invertebrate community are not well understood and vary across studies and taxonomic levels. The aim of this study was to investigate the effects of reed harvest on invertebrate communities. Ground-dwelling and aerial invertebrates were continuously sampled for 10 weeks in the largest coherent reed bed of Scandinavia in order to assess how time since last reed harvest (0, 3, and 25-years) influences invertebrate biomass, biodiversity and community structure across taxonomic levels. Biomass was measured and all specimens were sorted to order level, and Coleoptera was even sorted to species level. The invertebrate community showed distinct compositional differences across the three reed bed ages. Furthermore, biomass of both aerial and ground-dwelling invertebrates was highest in the age-0 reed bed and lowest in the age-25 reed bed. Generally, biodiversity showed an opposite trend with the highest richness and diversity in the age-25 reed bed. We conclude that it is possible to ensure high insect biomass and diversity by creating a mosaic of reed bed of different ages through small-scale harvest in the largest coherent reed bed in Scandinavia. The youngest red beds support a high invertebrate biomass whereas the oldest reed beds support a high biodiversity. Collectively, this elevate our understanding of reed harvest and the effects it has on the invertebrate communities, and might aid in future reed bed management and restoration.

Identifying forcing agents of environmental change and ecological response on the Mississippi River Delta, Southeastern Louisiana

Freshwater wetlands on the Mississippi River delta plain, containing extensive swamps and marshes, have experienced land loss of 5197 km² since the 1930s as the ocean has transgressed landward, resulting in landward retreat of bottomland forest, and transition of fresh to intermediate marsh. The timing and rapidity of these ecotonal transitions, and the impacts of natural and anthropogenic forces on this deltaic environment are uncertain. This study details a 448 cm sediment core retrieved from the intermediate marsh on the northern edge of Lake Salvador in southeastern Louisiana. Multi-proxy data identify six ecological shifts since 3500 BP. The ecosystem has shifted from interdistributary environment with high concentrations of such terrestrial and marine elements as Ca, Zr (3.5-3.0 cal kyr BP), to a freshwater deltaic-plain with an increase in freshwater herbs and trees (3.0-2.6 cal kyr BP), to a lacustrine environment marked by high Mn, Fe concentrations (2.6-2.2 cal kyr BP), to a swamp ecosystem with high concentrations of Zn, Br (2.2-1.4 cal kyr BP), to freshwater marsh with an increase in marsh plants (1.4-0.3 cal kyr BP), and to an intermediate marsh marked by Typha and Baccharis with elevated marine elements (since 0.3 cal kyr BP). The study identified the external forcing agents driving each deltaic environmental transition using multivariable analyses. Ecosystem dynamics are highly associated with the St. Bernard deltaic cycles, with dominant fluvial processes introducing freshwater ecosystems while forming geomorphological features such as levees, oxbow lakes, and back swamp and marsh during delta progradation. Thereafter, reduced sediment supply and decreased freshwater flow during delta transgression caused land subsidence and uneven topography. As a result, the swamp converted to marsh. Eighteenth century logging and canal development by Activities from French and Spanish settlements reduced the cypress forests and enlarged the coastal lakes.

The dynamic land-cover of the Altai Mountains: Perspectives based on past and current environmental and biodiversity changes

We present climate-dependent changes in the high-mountain forest ecotone, old-growth forests, alpine phytocenoses, and deglaciated forelands in the Aktru glacial basin (Altai Republic, Russia). A number of independent sources (variations in upper treeline altitude, dendrochronological data, analysis of lacustrine sediments and botanical and geographical studies linked with the dynamics of glacial-dammed lakes in the Chuya and Kurai intermountain depressions) suggest Holocene temperatures reached about 4 °C higher than today. Unlike the European Alps, glaciers in the continental Altai Mountains disappeared before forming again. Also, the upper altitudinal limit of mountain forests during the Holocene was greater than in the European Alps. The high variability of mountain ecosystems in southern Siberia suggests their potential instability in a currently changing climate. However, periglacial successions associated with the strong continental climate and glacier retreat represent an area of increasing biodiversity and plant cover. The historical and current sensitivity of the continental mountains to climate variations which exceeds that of the European Alps requires greater understanding, environmental protection, and increased social responsibility for the consequences of anthropogenic contributions to climate change: the isolated Altai areas contribute little to climate changes, but are greatly affected by them.

Two facets of geotextiles in coastal ecosystems: Anti- or profouling effects?

Nonwoven geotextile fabrics have physical, mechanical and hydraulic properties useful in coastal protection as an alternative to natural stone, slag, and concrete. In a 10-month experiment, the colonisation of macrofouling organisms on different substrata based on polypropylene (PP), polyester (PET) or high density polyethylene (HDPE) fibres was investigated in the Lagoon of Venice, Italy - an environment with temperate transitional waters with high biodiversity - and compared with the colonisation on wood as a reference substratum, because of its occurrence in artificial structures at the study location, until a stable stage was reached in the development of the macrofouling community. Geotextile fabrics showed implications for community development. They affected both ecological succession in different ways by disturbing biofouling settlement and growth (HDPE fabrics) or favouring species which become dominant (PP fabrics). For these two-faceted aspects that potentially cause different long-term impacts on the biodiversity of resident communities, the use of geotextile fabrics as antifouling or as profouling systems for restoration of degraded ecosystems is discussed. In all cases, the communities displayed unique properties, such as differences in the settlement of pioneer species, an initial disturbance to serpulid settlement, absence of barnacles, selection of dominant taxa (ascidians), and changes in the percentages of various taxa forming the community structure. Given the increasing interest in geotextile materials for employment in various marine developments and industries, these results could represent first lines of evidence to inform decision-making to minimise/modify biofouling, and/or predict the use of artificial substrata as habitats by marine organisms.

Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome

Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.

Recovery of hydrothermal vent communities in response to an induced disturbance at the Lucky Strike vent field (Mid-Atlantic Ridge)

So far, the natural recovery of vent communities at large scales has only been evaluated at fast spreading centers, by monitoring faunal recolonisation after volcanic eruptions. However, at slow spreading ridges, opportunities to observe natural disturbances are rare, the overall hydrothermal system being more stable. In this study, we implemented a novel experimental approach by inducing a small-scale disturbance to assess the recovery potential of vent communities along the slow-spreading northern Mid-Atlantic Ridge (nMAR). We followed the recovery patterns of thirteen Bathymodiolus azoricus mussel assemblages colonising an active vent edifice at the Lucky Strike vent field, in relation to environmental conditions and assessed the role of biotic interactions in recolonisation dynamics. Within 2 years after the disturbance, almost all taxonomic richness had recovered, with the exception of a few low occurrence species. However, we observed only a partial recovery of faunal densities and a major change in faunal composition characterised by an increase in abundance of gastropod species, which are hypothesised to be the pioneer colonists of these habitats. Although not significant, our results suggest a potential role of mobile predators in early-colonisation stages. A model of post-disturbance succession for nMAR vent communities from habitat opening to climax assemblages is proposed, also highlighting numerous knowledge gaps. This type of experimental approach, combined with dispersal and connectivity analyses, will contribute to fully assess the resilience of active vent communities after a major disturbance, especially along slow spreading centers targeted for seafloor massive sulphide extraction.

Soil organic carbon accumulation rates on Mediterranean abandoned agricultural lands

Secondary succession on abandoned agricultural lands can produce climate change mitigation co-benefits, such as soil carbon sequestration. However, the accumulation of soil organic carbon (SOC) in Mediterranean regions has been difficult to predict and is subject to multiple environmental and land management factors. Gains, losses, and no significant changes have all been reported. Here we compile chronosequence data (n = 113) from published studies and new field sites to assess the response of SOC to agricultural land abandonment in peninsular Spain. We found an overall SOC accumulation rate of +2.3% yr^-1 post-abandonment. SOC dynamics are highly variable and context-dependent. Minimal change occurs on abandoned cereal croplands compared to abandoned woody croplands (+4% yr^-1). Accumulation is most prevalent within a Goldilocks climatic window of ~13-17 °C and ~450-900 mm precipitation, promoting >100% gains after three decades. Our secondary forest field sites accrued 40.8 Mg C ha^-1 (+172%) following abandonment and displayed greater SOC and N depth heterogeneity than natural forests demonstrating the long-lasting impact of agriculture. Although changes in regional climate and crop types abandoned will impact future carbon sequestration, abandonment remains a low-cost, long-term natural climate solution best incorporated in tandem with other multipurpose sustainable land management strategies.

The interplay of flow processes shapes aquatic invertebrate successions in floodplain channels - A modelling applied to restoration scenarios

The high biotic diversity supported by floodplains is ruled by the interplay of geomorphic and hydrological processes at various time scales, from daily fluctuations to decennial successions. Because understanding such processes is a key question in river restoration, we attempted to model changes in taxonomic richness in an assemblage of 58 macroinvertebrate taxa (21 gastropoda and 37 ephemeroptera, plecoptera and trichoptera, EPT) along two successional sequences typical for former braided channels. Individual models relating the occurrence of taxa to overflow and backflow durations were developed from field measurements in 19 floodplain channels of the Rhône floodplain (France) monitored over 10 years. The models were combined to simulate diversity changes along a progressive alluviation and disconnection sequence after the reconnection with the main river of a previously isolated channel. Two scenarios were considered: (i) an upstream + downstream reconnection creating a lotic channel, (ii) a downstream reconnection creating a semi-lotic channel. Reconnection led to a direct increase in invertebrate richness (on average x2.5). However, taxonomical richness showed a constant decrease as isolation progressed and reached an average of 2 for EPT and 7 for gastropods at the end of the scenarios. With more than 80% of the taxonomic models with an AUC equal or higher than 0.7 and slopes of linear relations between observed and predicted richness of 0.75 (gastropods) and 1 (EPT), the Boosted Regression Trees (BRT) provided a good basis for prediction of species assemblages. These models can be used to quantify a priori the sustainability and ecological efficiency of restoration actions and help floodplain restoration planning and management.

Fate of lost fishing gears: Experimental evidence of biofouling colonization patterns from the northwestern Mediterranean Sea

ALDFGs (abandoned, lost or otherwise discharged fishing gears) represent a major pollutant in the world's oceans, including the Mediterranean Sea, but very little is known about their long-term fate in the underwater environment. Here we investigate the destiny of ALDFGs in a coralligenous benthic community by studying the biofouling growing on them at 30 m depth over a three-year period. Results indicate that ALDFGs are quickly covered by biofouling, reaching maximum values of cover in one year. At this depth, the biofouling community results highly influenced by light-dependent seasonal cycles and a general four-steps colonization scheme is tentatively depicted: i) biofouling community is initially dominated by fast-growing organisms, with algae and hydrozoans settling after two weeks; ii) small-sized carbonatic organisms (e.g. bryozoans) appear after two months; iii) the same organisms (including coralline algae) become abundant after five to eight months; iv) conspicuous carbonatic skeletons (serpulids, bivalves and bryozoans) occur after one year increasing in complexity in the following months. The biofouling settled on ALDFGs, as well as growth rates of large carbonatic species, could provide useful information to estimate the age of lost lines and nets in retrieved material and in situ photo footage complementing the overview of the fishing impact in this specific environment. Finally, no signs of nylon degradation are reported, suggesting that the prevailing physical conditions and the biofouling cover extent could alter microplastics release from nylon ALDFGs.

Integrating microbial metagenomics and physicochemical parameters and a new perspective on starter culture for fine cocoa fermentation

Cocoa beans used for chocolate production are fermented seeds of Theobroma cacao obtained by a natural fermentation process. The flavors and chemical compounds produced during the fermentation process make this step one of the most important in fine chocolate production. Herein, an integrative analysis of the variation of microbial community structure, using a shotgun metagenomics approach and associated physicochemical features, was performed during fermentation of fine cocoa beans. Samples of Forastero variety (FOR) and a mixture of two hybrids (PS1319 and CCN51) (MIX) from Bahia, Brazil, were analyzed at 7 different times. In the beginning (0 h), the structures of microbial communities were very different between FOR and MIX, reflecting the original plant-associated microbiomes. The highest change in microbial community structures occurred at the first 24 h of fermentation, with a marked increase in temperature and acetic acid concentration, and pH decrease. At 24-48 h both microbial community structures were quite homogenous regarding temperature, acetic acid, succinic acid, pH, soluble proteins and total phenols. During 72-96 h, the community structure resembles an acidic and warmer environment, prevailing few acetic acid bacteria. Taxonomic richness and abundance at 72-144 h exhibited significant correlation with temperature, reducing sugars, succinic, and acetic acids. Finally, we recommend that dominant microbial species of spontaneous fine cocoa fermentations should be considered as inoculum in accordance with the farm/region and GMP to maintain a differential organoleptic feature for production of fine chocolate. In our study, a starter inoculum composed of Acetobacter pausterianus and Hanseniaspora opuntiae strains is indicated.

The importance of edaphic niches functionality for the sustainability of phytomanagement in semiarid mining impacted ecosystems

Mining activities on metal sulphide ores are considered one of the most environmentally damaging anthropogenic activities worldwide, mainly due to the production of metal(loid)- enriched tailings. The objective of the work was to elucidate which factors, including edaphic, vegetation and microbiological aspects, determine soil functionality in the phytomagement of mine tailings piles in semiarid areas. For this purpose, a field study was conducted using a transect experimental design in a former mining area located in southern Spain. Soil characteristics, including edaphic parameters, bacterial and fungal compositions, were determined. The variation in edaphic parameters (pH, electrical conductivity, organic carbon, particle size distribution, etc) through the deterioration transect caused a decrease in plant and microbial diversities, as well as in microbial productivity measured by enzymatic activities. Variation in bacterial relative abundances through the transect was better explained by soil fertility related factors, such as organic matter, pH, salinity, enzymatic activities or microbial biomass (which in turn were related to the presence of plants), than by metals concentrations. The presence of vegetation at the tailings allowed the transition from lithotrophic bacterial orders which dominated in bare tailings areas (e.g. Acidimicrobiales, Chromatiales) to organotrophic oriented orders (e.g. Cytophagales, Actinomycetales). Vegetated patches at the tailings pile and its borders shared some organotrophic bacteria with control forest samples (e.g. Rhizobiales), indicating that natural plant mediated successional processes might stimulate biogeochemical cycles similar to those occurring at non-polluted systems. This functionality of the impacted sites, which include unfavourable edaphic conditions, should be taken into account in the phytomanagement of mine tailings, since it may support its long-term sustainability. Unlike bacteria, variations in fungal relative abundances through the transect were not clearly explained by soil parameters or the presence of plants. Other factors related to spatial distribution or the type of organic substrates may be more determinant in the case of fungi.

Dispersal mitigates bacterial dominance over microalgal competitor in metacommunities

Ecological theory suggests that a combination of local and regional factors regulate biodiversity and community functioning in metacommunities. The relative importance of different factors structuring communities likely changes over successional time, but to date this concept is scarcely documented. In addition, the few studies describing successional dynamics in metacommunity regulation have only focused on a single group of organisms. Here, we report results of an experimental study testing the effect size of initial local community composition and dispersal between local patches on community dynamics of benthic microalgae and their associated bacteria over community succession. Our results show that over time dispersal outweighed initial effects of community composition on microalgal evenness and biomass, microalgal β-diversity, and the ratio of bacteria to microalgae. At the end of the experiment (ca. 20 microalgae generations), dispersal significantly decreased microalgal evenness and β-diversity by promoting one regionally superior competitor. Dispersal also decreased the ratio of bacteria to microalgae, while it significantly increased microalgal biomass. These results suggest that the dispersal-mediated establishment of a dominant and superior microalgae species prevented bacteria from gaining competitive advantage over the autotrophs in these metacommunities, ultimately maintaining the provision of autotrophic biomass. Our study emphasizes the importance of time for dispersal to be a relevant community-structuring mechanism. Moreover, we highlight the need for considering multiple competitors in complex metacommunity systems to properly pinpoint the consequences of local change in dominance through dispersal for metacommunity function.

Divergence of riparian forest composition and functional traits from natural succession along a degraded river with multiple stressor legacies

Prolonged exposure to human induced-stressors can profoundly modify the natural trajectory of ecosystems. Predicting how ecosystems respond under stress requires understanding how physical and biological properties of degraded systems parallel or deviate over time from those of near-natural systems. Utilizing comprehensive forest inventory datasets, we used a paired chronosequence modelling approach to test the effects of long-term channelization and flow regulation of a large river on changes in abiotic conditions and related riparian forest attributes across a range of successional phases. By comparing ecological trajectories between the highly degraded Rhône and the relatively unmodified Drôme rivers, we demonstrated a rapid, strong and likely irreversible divergence in forest succession between the two rivers. The vast majority of metrics measuring life history traits, stand structure, and community composition varied with stand age but diverged significantly between rivers, concurrent with large differences in hydrologic and geomorphic trajectories. Channelization and flow regulation induced a more rapid terrestrialization of the river channel margins along the Rhône River and accelerated change in stand attributes, from pioneer-dominated stands to a mature successional phase dominated by non-native species. Relative to the Drôme, dispersion of trait values was higher in young forest stands along the Rhône, indicating a rapid assembly of functionally different species and an accelerated transition to post-pioneer communities. This study demonstrated that human modifications to the hydro-geomorphic regime have induced acute and sustained changes in environmental conditions, therefore altering the structure and composition of riparian forests. The speed, strength and persistence of the changes suggest that the Rhône River floodplain forests have strongly diverged from natural systems under persistent multiple stressors during the past two centuries. These results reinforce the importance of considering historical changes in environmental conditions to determine ecological trajectories in riparian ecosystems, as has been shown for old fields and other successional contexts.

Ecological succession and resilience of plankton recovering from an acute disturbance in freshwater marshes

The increase in extreme events such as storms is one of the major threats that coastal ecosystems will have to face in the near future. In such a context, both maturation and ecological successions processes remain at the core of ecology to better anticipate the changes to ecosystem biodiversity and functions facing environmental stressors. However, these concepts are mainly approached through closed experimental studies that oversimplify the mechanisms. A survey was carried out on a 'natural' and open ecosystem subjected to an acute disturbance, i.e. a marine submersion of freshwater drained marshes, occurring after a storm. Plankton biomass, production and taxonomic/functional phytoplankton diversity were followed weekly at four stations over 2 months. Most of the stations were disrupted by this acute disturbance and displayed gradual growth and development, as described in the classical maturation process. The main differences between stations were attributed to the heterogeneity of the communities before the storm, the intensity of the disturbance and the different human actions performed to recover the freshwater environment. The concept of 'ecological resilience' was thus better suited than 'engineering resilience' for such open systems facing constant fluctuations in environmental drivers. With regard to ecological succession, the more impacted stations were marked by a significant change in taxonomic beta-diversity, with numerous stochastic processes, due to taxa dispersion. They first exhibited a convergence in functional traits due to the increase in nutrient availability drained from the catchment basin and then an increase in divergence when nutrients became limited.

A succession of marine bacterial communities in batch reactor experiments during the degradation of five different petroleum types

Marine microbial communities might be subjected to accidental petroleum spills; however, some bacteria can degrade it, making these specific bacteria valuable for bioremediation from petroleum contamination. Thus, characterizing the microbial communities exposed to varying types of petroleum is essential. We evaluated five enriched microbial communities from the northwest Gulf of Mexico (four from the water column and one from sediments). Enrichments were performed using five types of petroleum (extra light, light, medium, heavy and extra heavy), to reveal the microbial succession using a 16S rDNA amplicon approach. Four communities were capable of degrading from extra light to heavy petroleum. However, only the community from sediment was able to degrade the extra heavy petroleum. Successional changes in the microbial communities' structures were specific for each type of petroleum where genus Dietzia, Gordonia, Microvirga, Rhizobium, Paracoccus, Thalassobaculum, Sphingomonas, Moheibacter, Acinetobacter, Pseudohongiella, Porticoccus, Pseudoalteromonas, Pseudomonas, Shewanella, and Planctomyces presented differential abundance between the treatments.

Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits

Plant species identity is assumed to be a major driver of belowground microbial diversity and composition. However, diagnosing which plant functional traits are responsible for shaping microbial communities remains elusive. Primary succession on barren metalliferous mining substrates was selected as the framework to study above-belowground interactions, and plant functional traits that lead the successional trajectories of soil bacterial communities were identified. The impact of the plant functional group (i.e. trees, shrubs, dwarf shrubs, perennial grasses), a trait integrating the life span and morphological structure, on the bacterial primary succession was monitored. Bacterial diversity and composition was estimated along plant size gradients including over 90 scattered patches ranging from seedlings to mature multispecific patches. Soil bacterial diversity was affected by heavy metals levels and increased towards higher resource availability underneath mature patches, with stress-tolerant heterotrophs and phototrophs being replaced by competitive heterotrophs. The plant functional group modulated these general patterns and shrubs had the greatest impact belowground by inducing the largest increase in soil fertility. Functional traits related to leaf decomposability and root architecture further determined the composition and structure of bacterial communities. These results underline the importance of plant functional traits in the assembly of soil bacterial communities, and can help guiding restoration of degraded lands.

Understanding microbial community dynamics to improve optimal microbiome selection

BACKGROUND

Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown.

RESULTS

Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms.

CONCLUSIONS

The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.

Drivers of phytoplankton blooms in the northeastern Black Sea

In order to understand of the processes controlling phytoplankton successions in the NE Black Sea, long-term data series are needed. We compiled 15 years (2002-2017) of measurements from which the existence emerges of a tight link between phytoplankton species dominance and nutrients concentrations. The latter is strongly influenced by wind direction. The link between algal dominance and nutrients is mediated by the growth strategy adopted by algal species. In spring, when nutrients are abundant, small diatoms such as Pseudo-nitzschia pseudodelicatissima, with a "rapid growth strategy", prevail. In late spring and early summer, when N is low and P and Si are high, coccolithophorids such as Emiliania huxhleyi dominate, thanks to an "affinity growth strategy". Large diatoms, especially Pseudosolenia calcar-avis, dominate in summer and autumn, when their "storage growth strategy" allows the exploitation of discontinuous upwelling of nutrients. These seasonal changes of dominant species influence the structure of the food web.

Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence

Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.

Current conditions and colonization history asymmetrically shape the organization of shallow sessile communities after simulated state shifts

Historical processes affecting biological organization are rarely considered when predicting the effects of disturbance on community structure. In order to assess the relative importance of historical and post-disturbance conditions as determinants of community structure, we undertook reciprocal transplants, at different successional stages, of sessile communities developing at recreational piers that were previously observed to show contrasting fish predation pressure and settlement rate in the São Sebastião Channel, Brazil. Regardless the direction of state shift, after 15 weeks communities converged to the destination site structure, substantially drifting away from the path observed at origin, therefore revealing high susceptibility to environmental change. Although converging, transplanted communities never matched the destination standard in both transplant directions, suggesting that history still mattered, as providing some legacy that lasted, at least, for 15 weeks. The taxonomic groups resisting community drift were hard-bodied invertebrates, which could eventually provide some resilience to these communities through ecosystem engineering.

Searching for putative avian malaria vectors in a Seasonally Dry Tropical Forest in Brazil

Background

Haemosporidian parasites of the genera Plasmodium and Haemoproteus can have detrimental effects on individual birds and populations. Despite recent investigations into the distribution and richness of these parasites and their vertebrate hosts, little is known about their dipteran vectors. The Neotropics has the highest diversity of mosquitoes in the world, but few studies have tried to identify vectors in this area, hampering the understanding of the ecology of avian malaria in the highly diverse Neotropical environments.

Methods

Shannon traps and active collection were used to capture 27,110 mosquitoes in a Seasonally Dry Tropical Forest in southeastern Brazil, a highly endangered ecosystem.

Results

We screened 17,619 mosquito abdomens from 12 different species and several unidentified specimens of Culex, grouped into 1,913 pools, for the presence of haemosporidians. Two pools (out of 459) of the mosquito Mansonia titillans and one pool (out of 29) of Mansonia pseudotitillans were positive for Plasmodium parasites, with the detection of a new parasite lineage in the former species. Detected Plasmodium lineages were distributed in three different clades within the phylogenetic tree revealing that Mansonia mosquitoes are potential vectors of genetically distant parasites. Two pools of Culex spp. (out of 43) were positive for Plasmodium gallinaceum and closely related lineages. We found a higher abundance of these putative vectors in pasture areas, but they were also distributed in areas at intermediate and late successional stages. One pool of the mosquito Psorophora discrucians (out of 173) was positive for Haemoproteus.

Conclusions

The occurrence of different Plasmodium lineages in Mansonia mosquitoes indicates that this genus encompasses potential vectors of avian malaria parasites in Brazil, even though we did not find positive thoraces among the samples tested. Additional evidence is required to assign the role of Mansonia mosquitoes in avian malaria transmission and further studies will add information about evolutionary and ecological aspects of avian haemosporidia and untangle the diversity of their vectors in Brazil.

Effects of organic pollution on biological communities of marine biofilm on hard substrata

We examined the effect of organic enrichment on diatom and bacterial assemblages of marine epilithic biofilms on two locations in the Mediterranean, one situated in Spain and the other in Greece. Total organic carbon, total organic nitrogen, stable isotopes (δ(13)C and δ(15)N) and chlorophyll a indicated significant incorporation of organic wastes, increased primary production and trophic niche modifications on the biofilms close to the organic enrichment source. In Spain, where the organic load was higher than in Greece, diatom and, to some extent, bacterial assemblages varied following the organic enrichment gradient. The taxonomic richness of diatom and bacterial communities was not influenced by organic enrichment. Classical community parameters showed consistent patterns to organic pollution in both locations, whereas community assemblages were only influenced when organic pollution was greatest. The successional patterns of these communities were similar to other epilithic communities. The modification of community assemblages induced by organic pollution may affect ecological functions.

Changes in tolerance to herbicide toxicity throughout development stages of phototrophic biofilms

Ecotoxicological experiments have been performed in laboratory-scale microcosms to investigate the sensitivity of phototrophic biofilm communities to the alachlor herbicide, in relation to the stages of phototrophic biofilm maturation (age of the phototrophic biofilms) and physical structure (intact biofilm versus recolonization). The phototrophic biofilms were initially cultivated on artificial supports in a prototype rotating annular bioreactor (RAB) with Taylor-Couette type flow under constant operating conditions. Biofilms were collected after 1.6 and 4.4 weeks of culture providing biofilms with different maturation levels, and then exposed to nominal initial alachlor concentration of 10 μg L(-1) in either intact or recolonized biofilms for 15 days in microcosms (mean time-weighted average concentration - TWAC of 5.52 ± 0.74 μg L(-1)). At the end of the exposure period, alachlor effects were monitored by a combination of biomass descriptors (ash-free dry mass - AFDM, chlorophyll a), structural molecular fingerprinting (T-RFLP), carbon utilization spectra (Biolog) and diatom species composition. We found significant effects that in terms of AFDM, alachlor inhibited growth of the intact phototrophic biofilms. No effect of alachlor was observed on diatom composition or functional and structural properties of the bacterial community regardless of whether they were intact or recolonized. The intact three-dimensional structure of the biofilm did not appear to confer protection from the effects of alachlor. Bacterial community structure and biomass level of 4.4 weeks - intact phototrophic biofilms were significantly influenced by the biofilm maturation processes rather than alachlor exposure. The diatom communities which were largely composed of mobile and colonizer life-form populations were not affected by alachlor. This study showed that the effect of alachlor (at initial concentration of 10 μg L(-1) or mean TWAC of 5.52 ± 0.74 μg L(-1)) is mainly limited to biomass reduction without apparent changes in the ecological succession trajectories of bacterial and diatom communities and suggested that carbon utilization spectra of the biofilm are not damaged resulting. These results confirmed the importance of considering the influence of maturation processes or community age when investigating herbicide effects. This is particularly important with regard to the use of phototrophic biofilms as bio-indicators.