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52 results for “bioturbation”
Data from: Bioturbation determines the response of benthic ammonia oxidising microorganisms to ocean acidification
Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms.
Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments
In marine environments, macrofauna living in or on the sediment surface may alter the structure, diversity and function of benthic microbial communities. In particular, microbial nitrogen (N)-cycling processes may be enhanced by the activity of large bioturbating organisms. Here, we study the effect of the burrowing mud shrimp Upogebia deltaura upon temporal variation in the abundance of genes representing key N-cycling functional guilds. The abundance of bacterial genes representing different N-cycling guilds displayed different temporal patterns in burrow sediments in comparison with surface sediments, suggesting that the burrow provides a unique environment where bacterial gene abundances are influenced directly by macrofaunal activity. In contrast, the abundances of archaeal ammonia oxidizers varied temporally but were not affected by bioturbation, indicating differential responses between bacterial and archaeal ammonia oxidizers to environmental physicochemical controls. This study highlights the importance of bioturbation as a control over temporal variation in nitrogen-cycling microbial community dynamics within coastal sediments.
Data from: The effect of bioturbation by polychaetes (Opheliidae) on benthic foraminiferal assemblages and test preservation
Biological activity such as burrowing can alter benthic foraminiferal shell preservation and may also modify benthic foraminiferal assemblages by vertical mixing, inducing sediment homogenization. Here, we analyse benthic foraminiferal assemblages and taphonomy of upper Miocene marine deposits from Conil de la Frontera (Cádiz, south-western Spain). The deposits consist of marls displaying a pervasive alternation of intensively bioturbated beds dominated by Macaronichnus segregatis traces (ichnofabric index 4–5) and non-bioturbated beds. Benthic foraminiferal assemblages are dominated by Cibicidoides mundulus and Cibicides refulgens, indicating that the marls were deposited on an oligotrophic, well-oxygenated upper slope. The impact of burrowing on the preservation of benthic foraminiferal tests was tested using Q-mode cluster analysis, which found two well-differentiated groups of samples, one including the non-bioturbated beds and the other encompassing the bioturbated ones. Fragmentation and recrystallization account for the differentiation of these groups, both being higher in the bioturbated sediments. Aggressive chemical digestion by the Macaronichnus trace-makers, assumed to be a polychaete worm of the family Opheliidae, etched the microfossil shells, making them more vulnerable to fragmentation. Intense bioturbation favoured the circulation of pore fluids, encouraging recrystallization. Pervasive burrowing resulted in significant vertical reworking of microfossils. As a consequence, benthic foraminiferal assemblages in the bioturbated beds were homogenized in the mixed layer; that is, the uppermost layer of the substrate totally burrowed. The alternation of bioturbated and non-bioturbated beds reflects episodic transfer of food particles down slope from shallower parts of the shelf as well as from the continent due to storms under otherwise homogeneous oligotrophic marine conditions.
Data from: How the litter-feeding bioturbator Orchestia gammarellus promotes late successional salt marsh vegetation
1.Traditionally, studies on vegetation succession have focused either on plant-plant interactions, or on interactions between plants and their physical environment, e.g. through organic matter build-up and increased nutrient cycling. These interactions can change conditions for macrodetritivores that feed on plant litter, but their role in vegetation succession is rarely studied. In this paper we explore whether the bioturbating crustacean macrodetritivore Orchestia gammarellus alters soil conditions in a salt marsh ecosystem in such a way that it promotes late successional, less stress-tolerant plant species at the expense of early successional species. 2.To answer this, we performed a field and a laboratory experiment in which we manipulated abundances of O. gammarellus, and studied the consequences for soil physical and chemical parameters and for vegetation community composition. 3.Our field experiment showed that O. gammarellus stimulated nitrogen mineralization, likely resulting from the positive effect of this macrodetritivore on soil aeration and litter decomposition. Moreover, results from the laboratory experiment showed that O. gammarellus negatively affected dicot seedling survival of mainly early successional plant species, likely through grazing, thus affecting plant community composition. 4.The experiments together provided evidence that O. gammarellus promotes late successional plant species in multiple ways: by alleviation of anoxic conditions, by promoting nutrient cycling and by selective herbivory on early successional species. 5.Synthesis: By demonstrating that a species traditionally considered as part of the detrital ('brown') food web is thus an important accelerator of vegetation succession, this study documents an important but often overlooked link in food web and ecosystem ecology.
FIGURE 8 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 8. Consumption of local baited fish (vertebral columns of Trachurus trachurus (Linnaeus, 1758) and skin of undetermined deep-sea shark) by benthic scavengers (mainly Politolana sanchezi sp. nov.) during a 12h TFS night trophic experiment on the bottom of the Cantabrian continental slope (15–16/04/2004, 602 m depth). (Photo: F. Sánchez).
FIGURE 4 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 4. Politolana sanchezi sp. nov., (A–G) paratype male (MNCN 20.04/8351); posterior face of left pereopods: (A) pereopod 1, (B) pereopod 2, (C) pereopod 3, (D) pereopod 4, (E) pereopod 5, (F) pereopod 6, (G) pereopod 7. Scale bar: 1 mm.
FIGURE 3 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 3. Politolana sanchezi sp. nov., (A) holotype male (MNCN 20.04/8350); (B–G) paratype male (MNCN 20.04/ 8351); (A) frontal lamina, clypeus and labrum, (B) antennule, (C) antenna, (D) dorsal view of left mandible, (E) dorsal view of left maxillule, (F) dorsal view of left maxilla, (G) dorsal view of left maxilliped. Scale bars: 1 mm.
FIGURE 2 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 2. Politolana sanchezi sp. nov., (A) lateral and (B) dorsal views of holotype male (MNCN 20.04/8350); (C) pleotelson apex of paratype male (MNCN 20.04/8351) in dorsal view. Scale bars: A–B = 5 mm, C = 0.1 mm.
FIGURE 1 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 1. Geographical location of sampling stations where the isopod Politolana sanchezi sp. nov. was collected in the southeastern Bay of Biscay. Square: suprabenthic sledge; rhombus: fish-baited trap mounted on photogrammetric sledge; triangle: Flusha box corer.
FIGURE 5 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 5. Politolana sanchezi sp. nov., (A–C) paratype male (MNCN 20.04/8352), (D) paratype male (MNCN 20.04/ 8351); posterior face of left pleopods: (A) pleopod 1, (B) pleopod 2, (C) pleopod 5; (D) ventral view of left uropod. Scale bars: 1 mm.
FIGURE 7 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 7. Bioturbation of surficial sediments related to the scavenging behaviour of benthic crustaceans (mainly represented by the isopod Politolana sanchezi sp. nov.) during a 12h TFS night trophic experiment on the Cantabrian continental slope (15–16/04/2004, 602 m depth). A: photo n°1 (20h18) showing the initial bottom aspect with regular ripple marks at the beginning of the sequence. B: photo n° 20 (23h30) showing numerous isopods attracted by the baited fish of the trap, the disappearance of ripple marks in the area close to the sledge where the bioturbating activity of scavengers is maximal, the cloudy aspect of the near-bottom water just above the bioturbated area due to the presence of resuspended muddy bottom particles. (Photos: F. Sánchez).
FIGURE 6 in Politolana sanchezi sp. nov. (Crustacea: Isopoda: Cirolanidae), a new benthic bioturbating scavenger from bathyal soft-bottoms of the southern Bay of Biscay (northeastern Atlantic Ocean)
FIGURE 6. Geographical distribution of Politolana species, based on data from Wetzer et al. 1986, Riseman et al. 2001, 2002. Each species symbol on the planisphere is located at the sampling station of the corresponding holotype, except for P. eximia (original station not known; symbol positioned centrally on the Brazilian coast).
Ecosystem roles and conservation status of bioturbator mammals
<p>The action of biological reworking of soils is referred to as bioturbation, and many species of mammals globally have an important role in soil disturbance, modifying ecosystem characteristics.</p> <p>We examined global patterns in the distribution, conservation status, and threats to the world's bioturbator mammals and illustrated the relevant roles these species play in ecosystem engineering related to soil processes and services. We searched the data available on 3932 non‐flying land‐dwelling mammals included in the International Union for Conservation of Nature's (IUCN) Red List.</p> <p>Using existing literature and online databases, we determined that 869 (22%) of the non‐flying land‐dwelling mammals accessed can be considered as bioturbators in three distinct groups: foragers (<em>n = </em>123), semi‐fossorial species (<em>n = </em>652), and strictly fossorial species (<em>n = </em>94). Of the world's bioturbator mammal species, 16% are threatened, 2% are already Extinct, and 8% are classified as Data Deficient. Foragers have the highest percentage of threatened (35%) and Extinct (5%) species, while strictly fossorial species have the highest percentage of Data Deficient species (12%). Although the majority of bioturbator mammal species are found in Asia (32%), Oceania is the continent with the highest percentage of threatened (27%) and Extinct (11%) bioturbator species, while Central and South America have the highest percentage of species classified as Data Deficient (24%). The threats experienced by the greatest number of bioturbator mammal species are activities related to agriculture and aquaculture (29%), and biological resource use (22%).</p> <p>Soil bioturbation can improve ecosystem health by reducing soil compaction, increasing nutrient cycling, soil moisture, microbe diversity, plant recruitment, and carbon storage. The loss of bioturbator mammals could trigger cascading effects throughout the ecosystems they inhabit. A better understanding of their conservation status is important so that effective conservation measures can be developed.</p>
Fig. 2 in MaNgROVIVIRga CUNICULI gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family MaNgROVIVIRgaCeae fam. nov.
Fig. 2. (a) Maximum-likelihood phylogenetic tree based on the 16S rRNA gene sequences presenting the position of Mangrovivirga cuniculi R1DC9T (MT146883). Only bootstrap values (expressed as percentages of 1000 replications) exceeding 50% are shown at branching points. Psychroflexus torquis ATCC 700755T (GenBank accession no. U85881) was used as an outgroup. Bar, 0.040 substitutions per nucleotide position. Filled circles indicate branches that were also recovered using the neighbour-joining method. (b) Maximumlikelihood phylogenetic tree highlighting the position of R1DC9T relative to the other type strains within the order Cytophagales, including members of the families Marivirgaceae, Roseivirgaceae, Reichenbachiellaceae, Fulvivirgaceae, Cesiribacteraceae and Flammeovirgaceae. The phylogenetic tree was built using 120 concatenated single-copy genes obtained using GTDB-Tk software [34]. Bootstrap values greater than 50% based on 1000 replications are indicated at branching nodes. Bar, 0.2 substitutions per nucleotide position.
Fig. 1 in MaNgROVIVIRga CUNICULI gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family MaNgROVIVIRgaCeae fam. nov.
Fig. 1. (a) Sediments in the mangrove forest at KAUST bioturbated by Uca species crabs; crab barrows are indicated by yellow arrows. Leaves forming mangrove litter are also visible. Bar, 10 cm. (b) Aquarium filled with mangrove bioturbated sediments and FSW for the incubation of DCs; bar, 6 cm. (c) Aerial view of DCs placed on the surface of mangrove sediments and cover with FSW inside the aquarium; bar, 6 cm.
Bioturbation by endogeic earthworms facilitates entomopathogenic nematode movement toward herbivore-damaged maize roots
<p>Entomopathogenic nematodes (EPNs) have been extensively studied as potential biological control agents against root-feeding crop pests. Maize roots under rootworm attack have been shown to release volatile organic compounds, such as (E)-β-caryophyllene (Eβc) that guide EPNs toward the damaging larvae. As yet, it is unknown how belowground ecosystems engineers, such as earthworms, affect the biological control capacity of EPNs by altering the root Eβc-mediated tritrophic interactions. We here asked whether and how, the presence of endogeic earthworms affects the ability of EPNs to find root-feeding larvae of the beetle Diabrotica balteata. First, we performed a field mesocosm experiment with two diverse cropping systems, and revealed that the presence of earthworms increased the EPN infection potential of larvae near maize roots. Subsequently, using climate-controlled, olfactometer-based bioassays, we confirmed that EPNs response to Eβc alone (released from dispensers) was two-fold higher in earthworm-worked soil than in earthworm-free soil. Together our results indicate that endogeic earthworms, through burrowing and casting activities, not only change soil properties in a way that improves soil fertility but may also enhance the biocontrol potential of EPNs against root feeding pests. For an ecologically-sound pest reduction in crop fields, we advocate agricultural practices that favour earthworm community structure and diversity.</p>
Alternative combinations of tillage practices and crop rotations can foster earthworm density and bioturbation
<p><span>Earthworms, which contribute to important soil functions, suffer from intensive agriculture. Their response depends among other things on the earthworm ecological group (anecic, endogeic, epigeic) and the combination of the applied farming practices. To advice on methodological adaptations that enhance earthworm-mediated soil functions, effects of different practices on earthworms need to be studied in concert. We investigated the effects of tillage intensity (conventional, reduced, no tillage) and crop rotation diversity (simple = wheat, barley; diverse = wheat, peas, oil seed rape) on earthworm density and community composition in a Swedish long-term experiment. Furthermore, we calculated annual earthworm bioturbation to quantify the effects of farming practices on earthworm functions. Total earthworm densities did not vary between the different tillage intensities, but were on average 58% higher in the diverse than in the simple crop rotation. The pattern was mainly due to the response of the most abundant endogeic earthworms, which were not affected by tillage intensity, but were nearly two times more abundant in the diverse than in the simple crop rotation. Densities of anecic earthworms were 17 times higher under no tillage than conventional tillage. Anecic earthworms also benefitted from a diversified crop rotation, but the response depended on tillage intensity. The level of bioturbation reflected the response of anecic earthworms, and was more than</span><span> four times higher under no tillage, 549 g dw m -2 year -1, than under conventional tillage. We conclude that highest earthworm bioturbation is best achieved with no tillage. However, earthworm densities and potentially bioturbation can be increased also by a diversified crop rotation, when reducing tillage intensity is not feasible.</span></p>
Global distribution and environmental correlates of marine bioturbation
<p>This repository contains the R scripts necessary for conducting the data analysis for the paper titled 'Global distribution and environmental correlates of marine bioturbation', authored by Shuang Zhang, Martin Solan, and Lidya Tarhan.</p> <p>It includes five R files, which should be executed in the following order:</p> <p>01-Db_L_data_compilation: Initial data exploration and compilation (calculating average Db and L over time)</p> <p>02-Db_L_data_explore: Further data exploration and analysis</p> <p>03-Machine_learning_train: Building the machine learning framework</p> <p>04-Machine_learning_predict: Using the trained machine learning framework to predict global Db and L values</p> <p>05-MPA_analysis: Marine Protected Area (MPA) analysis</p> <p>The repository also contains all necessary data to run these scripts. In addition, this repository also contains the appendix figures for the bioturbation paper.</p>
The stable isotope data, and statistic of percentage of bioturbation and their halo from early Cambrian carbonate, North China
<p>The stable isotope data, and statistic of percentage of bioturbation and their halo from early Cambrian carbonate, North China</p>
Data from: The effect of bioturbation by polychaetes (Opheliidae) on benthic foraminiferal assemblages and test preservation
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